CHARMM Development Project
Posted By: Allen_123 Infinte ELEC energy of Drude simulation - 04/12/21 10:00 AM
Hello,

After setting up the drude system and creating the psf, I got NAN elec term when computing energy of a crystal. This causes error in minimization. But, there is no issue if I use C36m force field. The coordinates of system are exactly same except adding of the lone pairs and drude particles. So, it seems to me that it is not an issue of constrained system. I built the crystal from an asymmetric unit which was downloaded from Cambridge Crystallographic Data Center and used 2019 version Drude protein parameter set. Part of output is copied below:


........................................................................................................................
CHARMM> open read card name "prophephesingle.pdb" unit 21
VOPEN> Attempting to open::prophephesingle.pdb::
OPNLGU> Unit 21 opened for READONLY access to /home/yuxiang/work/prophephe/crystal/drude/setup/prophephesingle.pdb

CHARMM> read sequence card
MAINIO> Sequence information being read from unit 5.
RDTITL> * PRO-PHE-PHE TRIPEPTIDE
RDTITL> *

SEQRDR> 3

SEQRDR> PRO PHE PHE

RESIDUE SEQUENCE -- 3 RESIDUES
PRO PHE PHE

CHARMM> generate A last cter setup warn drude dmass 0.4
Drude polarizability will be setup for SEGID: A mass of Drudes particles = 0.4000
THE PATCH 'PROP' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 PRO .
ATOMS "N " "-C " "CA " "CD " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 PRO .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "O " "DO " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "C " "O " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "O " "LPOA " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "O " "LPOB " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "C " "CA " "+N " "O " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 3 PHE .
ATOMS "O " "C " WERE REQUESTED.

MKDRUDE generate list and setup for drude polarizability

All okay for 30 added Drude particles

GENPSF> Segment 1 has been generated. Its identifier is A.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 3
Number of atoms = 97 Number of groups = 5
Number of bonds = 97 Number of angles = 105
Number of dihedrals = 161 Number of impropers = 5
Number of cross-terms = 1
Number of HB acceptors = 2 Number of HB donors = 4
Number of NB exclusions = 0 Total charge = 0.00000
Number of Drudes = 30
Number of true-bonds = 97 Number of zero-bonds = 0
Number of aniso. terms = 4 Number of lone-pairs = 10

CHARMM> autogenerate angles dihedrals
AUTOGEN: All angles are removed and regenerated.
AUTOGEN: All dihedrals are removed and regenerated.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 3
Number of atoms = 97 Number of groups = 5
Number of bonds = 97 Number of angles = 105
Number of dihedrals = 161 Number of impropers = 5
Number of cross-terms = 1
Number of HB acceptors = 2 Number of HB donors = 4
Number of NB exclusions = 0 Total charge = 0.00000
Number of Drudes = 30
Number of true-bonds = 97 Number of zero-bonds = 0
Number of aniso. terms = 4 Number of lone-pairs = 10

CHARMM> read coor pdb unit 21
read CHARMM-pdb format
SPATIAL COORDINATES BEING READ FROM UNIT 21
TITLE> SINGLE PRO-PHE-PHE
TITLE> DATE: 8/24/20 11:42:24 CREATED BY USER: YUXIANG
TITLE> *

** WARNING ** For atom in coordinate file, the corresponding residue in the PSF lacks that atom:
INDEX= 2 IRES= 1 RESID=1 RES=PRO ATOM=HN1

** WARNING ** For atom in coordinate file, the corresponding residue in the PSF lacks that atom:
INDEX= 3 IRES= 1 RESID=1 RES=PRO ATOM=HN2
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 PRO DN
** WARNING ** After reading, there are no coordinates for selected atom: 3 1 PRO HT1
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 PRO HT2
** WARNING ** After reading, there are no coordinates for selected atom: 6 1 PRO DCD
** WARNING ** After reading, there are no coordinates for selected atom: 10 1 PRO DCA
** WARNING ** After reading, there are no coordinates for selected atom: 13 1 PRO DC
** WARNING ** After reading, there are no coordinates for selected atom: 15 1 PRO DO
** WARNING ** After reading, there are no coordinates for selected atom: 16 1 PRO LPOA
** WARNING ** After reading, there are no coordinates for selected atom: 17 1 PRO LPOB
** WARNING ** After reading, there are no coordinates for selected atom: 19 1 PRO DCB

** A total of 42 selected atoms have no coordinates
*** LEVEL 2 WARNING *** BOMLEV IS 0

CHARMM>

CHARMM> !ic purge ! CLEAN UP IC TABLE
CHARMM> !ic param ! GET MISSING IC DATA FROM PARAM FILE
CHARMM> !ic seed 1 N 1 CA 1 C
CHARMM> !ic build
CHARMM> coor sdrude

CHARMM> coor shake
SELECTED COORDINATES CONSTRAINED IN THE MAIN SET.


CHARMM> Hbuild select all end
SELRPN> 97 atoms have been selected out of 97
PRNHBD: CUToff Hydrogen Bond distance = 4.5000 Angle = 90.0000
CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000
CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000
ACCEptor antecedents included
All hydrogen bonds for each hydrogen will be found
Hydrogen bonds between excluded atoms will be kept


NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
874 874 873
: Ran out of space. RESIZING
with mode 5 found 608 exclusions and 420 interactions(1-4)
found 7 group exclusions.

CUToff Hydrogen Bond distance = 4.5000 Angle = 90.0000
CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000
CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000
ACCEptor antecedents included
dihedral PHI STePs for spin = 10.0000
cutoff for water acceptor search CUTWat= 4.5000

Place: HT1 ,HT2 , , constructed for donor A 1 PRO N .

CHARMM> coor print

COORDINATE FILE MODULE
TITLE> *SETUP FOR PROPHEPHE
TITLE> *
97 EXT
1 1 PRO N 3.7400000000 5.1270000000 6.8690000000 A 1 0.0000000000
2 1 PRO DN 3.7400000000 5.1270000000 6.8690000000 A 1 0.0000000000
3 1 PRO HT1 4.2710266859 4.3699982381 6.4276376574 A 1 0.0000000000
4 1 PRO HT2 2.7447969327 4.9346842611 6.7192427379 A 1 0.0000000000
5 1 PRO CD 4.0900000000 6.4200000000 6.1970000000 A 1 0.0000000000
6 1 PRO DCD 4.0900000000 6.4200000000 6.1970000000 A 1 0.0000000000
7 1 PRO HD1 3.2860000000 6.9840000000 6.0710000000 A 1 0.0000000000
8 1 PRO HD2 4.5130000000 6.2590000000 5.3160000000 A 1 0.0000000000
9 1 PRO CA 4.0620000000 5.2480000000 8.3200000000 A 1 0.0000000000
10 1 PRO DCA 4.0620000000 5.2480000000 8.3200000000 A 1 0.0000000000
11 1 PRO HA 4.8340000000 4.6510000000 8.5410000000 A 1 0.0000000000
12 1 PRO C 2.8560000000 4.8500000000 9.1540000000 A 1 0.0000000000
13 1 PRO DC 2.8560000000 4.8500000000 9.1540000000 A 1 0.0000000000
14 1 PRO O 1.7600000000 4.6660000000 8.6270000000 A 1 0.0000000000
15 1 PRO DO 1.7600000000 4.6660000000 8.6270000000 A 1 0.0000000000
16 1 PRO LPOA 1.8733577963 4.7299493126 8.3567029496 A 1 0.0000000000
17 1 PRO LPOB 1.6373112460 4.6004841763 8.8928103581 A 1 0.0000000000
18 1 PRO CB 4.4760000000 6.7110000000 8.5160000000 A 1 0.0000000000
19 1 PRO DCB 4.4760000000 6.7110000000 8.5160000000 A 1 0.0000000000
20 1 PRO HB1 3.6940000000 7.2800000000 8.7290000000 A 1 0.0000000000
21 1 PRO HB2 5.1490000000 6.8010000000 9.2360000000 A 1 0.0000000000
22 1 PRO CG 5.0660000000 7.0700000000 7.1600000000 A 1 0.0000000000
23 1 PRO DCG 5.0660000000 7.0700000000 7.1600000000 A 1 0.0000000000
24 1 PRO HG1 5.0990000000 8.0500000000 7.0300000000 A 1 0.0000000000
25 1 PRO HG2 5.9770000000 6.6960000000 7.0550000000 A 1 0.0000000000
26 2 PHE N 3.0720000000 4.7280000000 10.4660000000 A 2 0.0000000000
27 2 PHE DN 3.0720000000 4.7280000000 10.4660000000 A 2 0.0000000000
28 2 PHE HN 3.8910000000 4.7960000000 10.7820000000 A 2 0.0000000000
29 2 PHE CA 1.9620000000 4.4840000000 11.3780000000 A 2 0.0000000000
30 2 PHE DCA 1.9620000000 4.4840000000 11.3780000000 A 2 0.0000000000
31 2 PHE HA 1.3370000000 3.8370000000 10.9410000000 A 2 0.0000000000
32 2 PHE C 1.1870000000 5.7780000000 11.6580000000 A 2 0.0000000000
33 2 PHE DC 1.1870000000 5.7780000000 11.6580000000 A 2 0.0000000000
34 2 PHE O -0.0490000000 5.7570000000 11.7890000000 A 2 0.0000000000
35 2 PHE DO -0.0490000000 5.7570000000 11.7890000000 A 2 0.0000000000
36 2 PHE LPOA -0.0539280094 5.4603400961 11.7446309100 A 2 0.0000000000
37 2 PHE LPOB -0.0544836253 6.0534830072 11.8344725885 A 2 0.0000000000
38 2 PHE CB 2.4800000000 3.8440000000 12.6750000000 A 2 0.0000000000
39 2 PHE DCB 2.4800000000 3.8440000000 12.6750000000 A 2 0.0000000000
40 2 PHE HB1 3.1780000000 3.1800000000 12.4490000000 A 2 0.0000000000
41 2 PHE HB2 2.9000000000 4.5450000000 13.2340000000 A 2 0.0000000000
42 2 PHE CG 1.3910000000 3.1590000000 13.4820000000 A 2 0.0000000000
43 2 PHE DCG 1.3910000000 3.1590000000 13.4820000000 A 2 0.0000000000
44 2 PHE CD1 1.2260000000 1.7840000000 13.3820000000 A 2 0.0000000000
45 2 PHE DCD1 1.2260000000 1.7840000000 13.3820000000 A 2 0.0000000000
46 2 PHE HD1 1.8150000000 1.2830000000 12.8300000000 A 2 0.0000000000
47 2 PHE CD2 0.5220000000 3.8650000000 14.3050000000 A 2 0.0000000000
48 2 PHE DCD2 0.5220000000 3.8650000000 14.3050000000 A 2 0.0000000000
49 2 PHE HD2 0.6180000000 4.8070000000 14.3900000000 A 2 0.0000000000
50 2 PHE CE1 0.2170000000 1.1260000000 14.0730000000 A 2 0.0000000000
51 2 PHE DCE1 0.2170000000 1.1260000000 14.0730000000 A 2 0.0000000000
52 2 PHE HE1 0.1160000000 0.1850000000 13.9880000000 A 2 0.0000000000
53 2 PHE CE2 -0.4880000000 3.2150000000 15.0040000000 A 2 0.0000000000
54 2 PHE DCE2 -0.4880000000 3.2150000000 15.0040000000 A 2 0.0000000000
55 2 PHE HE2 -1.0720000000 3.7130000000 15.5640000000 A 2 0.0000000000
56 2 PHE CZ -0.6450000000 1.8490000000 14.8900000000 A 2 0.0000000000
57 2 PHE DCZ -0.6450000000 1.8490000000 14.8900000000 A 2 0.0000000000
58 2 PHE HZ -1.3370000000 1.4050000000 15.3660000000 A 2 0.0000000000
59 2 PHE LP 0.3635828073 2.4942590891 14.2003971280 A 2 0.0000000000
60 3 PHE N 1.9100000000 6.8800000000 11.7910000000 A 3 0.0000000000
61 3 PHE DN 1.9100000000 6.8800000000 11.7910000000 A 3 0.0000000000
62 3 PHE HN 2.7870000000 6.8170000000 11.7430000000 A 3 0.0000000000
63 3 PHE CA 1.3130000000 8.1950000000 12.0140000000 A 3 0.0000000000
64 3 PHE DCA 1.3130000000 8.1950000000 12.0140000000 A 3 0.0000000000
65 3 PHE HA 0.4700000000 8.2400000000 11.4780000000 A 3 0.0000000000
66 3 PHE C 2.2550000000 9.2860000000 11.4890000000 A 3 0.0000000000
67 3 PHE DC 2.2550000000 9.2860000000 11.4890000000 A 3 0.0000000000
68 3 PHE CB 0.9390000000 8.4280000000 13.4840000000 A 3 0.0000000000
69 3 PHE DCB 0.9390000000 8.4280000000 13.4840000000 A 3 0.0000000000
70 3 PHE HB1 0.4610000000 9.2920000000 13.5540000000 A 3 0.0000000000
71 3 PHE HB2 0.3110000000 7.7160000000 13.7650000000 A 3 0.0000000000
72 3 PHE CG 2.1040000000 8.4460000000 14.4490000000 A 3 0.0000000000
73 3 PHE DCG 2.1040000000 8.4460000000 14.4490000000 A 3 0.0000000000
74 3 PHE CD1 2.7170000000 9.6380000000 14.8320000000 A 3 0.0000000000
75 3 PHE DCD1 2.7170000000 9.6380000000 14.8320000000 A 3 0.0000000000
76 3 PHE HD1 2.4100000000 10.4600000000 14.4680000000 A 3 0.0000000000
77 3 PHE CD2 2.5990000000 7.2590000000 14.9890000000 A 3 0.0000000000
78 3 PHE DCD2 2.5990000000 7.2590000000 14.9890000000 A 3 0.0000000000
79 3 PHE HD2 2.2010000000 6.4340000000 14.7400000000 A 3 0.0000000000
80 3 PHE CE1 3.7730000000 9.6430000000 15.7380000000 A 3 0.0000000000
81 3 PHE DCE1 3.7730000000 9.6430000000 15.7380000000 A 3 0.0000000000
82 3 PHE HE1 4.1710000000 10.4660000000 15.9960000000 A 3 0.0000000000
83 3 PHE CE2 3.6640000000 7.2620000000 15.8830000000 A 3 0.0000000000
84 3 PHE DCE2 3.6640000000 7.2620000000 15.8830000000 A 3 0.0000000000
85 3 PHE HE2 3.9920000000 6.4410000000 16.2320000000 A 3 0.0000000000
86 3 PHE CZ 4.2480000000 8.4570000000 16.2660000000 A 3 0.0000000000
87 3 PHE DCZ 4.2480000000 8.4570000000 16.2660000000 A 3 0.0000000000
88 3 PHE HZ 4.9670000000 8.4620000000 16.8860000000 A 3 0.0000000000
89 3 PHE LP 3.1942607360 8.4509199492 15.3572226167 A 3 0.0000000000
90 3 PHE OT1 3.3970000000 8.9080000000 11.0840000000 A 3 0.0000000000
91 3 PHE DOT1 3.3970000000 8.9080000000 11.0840000000 A 3 0.0000000000
92 3 PHE OT2 1.8270000000 10.4560000000 11.5020000000 A 3 0.0000000000
93 3 PHE DOT2 1.8270000000 10.4560000000 11.5020000000 A 3 0.0000000000
94 3 PHE LPT1 3.5819080072 9.1836440250 10.9729621670 A 3 0.0000000000
95 3 PHE LPT2 3.4274982025 8.5610568968 11.1186459635 A 3 0.0000000000
96 3 PHE LPT3 2.0700586414 10.6737908554 11.3755498512 A 3 0.0000000000
97 3 PHE LPT4 1.5016958407 10.4630391819 11.6309482603 A 3 0.0000000000

CHARMM>

CHARMM> crystal define Monoclinic 5.3214 11.5689 17.0398 90 97.22 90
Crystal Parameters : Crystal Type = MONO
A = 5.32140 B = 11.56890 C = 17.03980
Alpha = 90.00000 Beta = 97.22000 Gamma = 90.00000

CHARMM> crystal build noper 1 cutoff 20
XBUILD> Building all transformations with a minimum atom-atom
contact distance of less than 20.00 Angstroms.

XBUILD> (-X,Y+1/2,-Z)

Range of Grid Search for Transformation 1 :
Lattice Vector A -6 TO 6
Lattice Vector B -3 TO 3
Lattice Vector C -2 TO 2


Range of Grid Search for Transformation 2 :
Lattice Vector A -5 TO 7
Lattice Vector B -4 TO 3
Lattice Vector C -1 TO 4


The number of transformations generated = 200


Number Symop A B C Distance

1 1 -4 0 -1 18.6999
2 1 -3 -1 -1 16.1549
3 1 -3 0 -1 14.6114
4 1 -3 1 -1 18.5257
5 1 -2 -2 -1 19.9433
6 1 -2 -1 -1 12.8348
7 1 -2 0 -1 10.8307
8 1 -2 1 -1 15.6480
9 1 -1 -2 -1 19.0434
10 1 -1 -1 -1 10.1085
11 1 -1 0 -1 6.9386
12 1 -1 1 -1 13.2721
13 1 -1 2 -1 19.9725
14 1 0 -2 -1 18.6091
15 1 0 -1 -1 9.2644
16 1 0 0 -1 5.9681
17 1 0 1 -1 10.7328
18 1 0 2 -1 18.8348
19 1 -4 -1 0 15.9549
20 1 -4 0 0 15.4147
21 1 -4 1 0 18.6005
22 1 -3 -2 0 17.6246
23 1 -3 -1 0 10.8976
24 1 -3 0 0 10.4003
25 1 -3 1 0 14.2655
26 1 -2 -2 0 14.7386
27 1 -2 -1 0 5.9059
28 1 -2 0 0 5.6659
29 1 -2 1 0 9.5827
30 1 -2 2 0 17.8504
31 1 -1 -2 0 13.1599
32 1 -1 -1 0 2.7631
33 1 -1 0 0 2.2198
34 1 -1 1 0 6.0549
35 1 -1 2 0 14.9106
36 1 0 -2 0 13.0630
37 1 0 -1 0 2.5236
38 1 0 1 0 2.5236
39 1 0 2 0 13.0630
40 1 -4 -1 1 19.0300
41 1 -4 0 1 18.3057
42 1 -3 -1 1 15.0696
43 1 -3 0 1 13.8784
44 1 -3 1 1 18.2200
45 1 -2 -2 1 19.7033
46 1 -2 -1 1 11.6937
47 1 -2 0 1 9.8924
48 1 -2 1 1 14.7232
49 1 -1 -2 1 18.6003
50 1 -1 -1 1 10.0613
51 1 -1 0 1 7.7293
52 1 -1 1 1 11.2300
53 1 -1 2 1 19.6617
54 1 0 -2 1 18.8348
55 1 0 -1 1 10.7328
56 1 0 0 1 5.9681
57 1 0 1 1 9.2644
58 1 0 2 1 18.6091
59 1 4 0 1 18.6999
60 1 3 1 1 16.1549
61 1 3 0 1 14.6114
62 1 3 -1 1 18.5257
63 1 2 2 1 19.9433
64 1 2 1 1 12.8348
65 1 2 0 1 10.8307
66 1 2 -1 1 15.6480
67 1 1 2 1 19.0434
68 1 1 1 1 10.1085
69 1 1 0 1 6.9386
70 1 1 -1 1 13.2721
71 1 1 -2 1 19.9725
72 1 4 1 0 15.9549
73 1 4 0 0 15.4147
74 1 4 -1 0 18.6005
75 1 3 2 0 17.6246
76 1 3 1 0 10.8976
77 1 3 0 0 10.4003
78 1 3 -1 0 14.2655
79 1 2 2 0 14.7386
80 1 2 1 0 5.9059
81 1 2 0 0 5.6659
82 1 2 -1 0 9.5827
83 1 2 -2 0 17.8504
84 1 1 2 0 13.1599
85 1 1 1 0 2.7631
86 1 1 0 0 2.2198
87 1 1 -1 0 6.0549
88 1 1 -2 0 14.9106
89 1 4 1 -1 19.0300
90 1 4 0 -1 18.3057
91 1 3 1 -1 15.0696
92 1 3 0 -1 13.8784
93 1 3 -1 -1 18.2200
94 1 2 2 -1 19.7033
95 1 2 1 -1 11.6937
96 1 2 0 -1 9.8924
97 1 2 -1 -1 14.7232
98 1 1 2 -1 18.6003
99 1 1 1 -1 10.0613
100 1 1 0 -1 7.7293
101 1 1 -1 -1 11.2300
102 1 1 -2 -1 19.6617
103 2 -1 -1 0 18.1067
104 2 -1 0 0 18.1067
105 2 0 -1 0 15.0986
106 2 0 0 0 15.0986
107 2 1 -2 0 19.9664
108 2 1 -1 0 13.0965
109 2 1 0 0 13.0965
110 2 1 1 0 19.9664
111 2 2 -2 0 19.9520
112 2 2 -1 0 13.1036
113 2 2 0 0 13.1036
114 2 2 1 0 19.9520
115 2 3 -1 0 15.1170
116 2 3 0 0 15.1170
117 2 4 -1 0 18.4927
118 2 4 0 0 18.4927
119 2 -3 -1 1 17.3544
120 2 -3 0 1 17.3544
121 2 -2 -2 1 16.6492
122 2 -2 -1 1 13.1647
123 2 -2 0 1 13.1647
124 2 -2 1 1 16.6492
125 2 -1 -2 1 13.1219
126 2 -1 -1 1 8.6741
127 2 -1 0 1 8.6741
128 2 -1 1 1 13.1219
129 2 0 -2 1 11.1268
130 2 0 -1 1 4.6012
131 2 0 0 1 4.6012
132 2 0 1 1 11.1268
133 2 1 -2 1 10.5085
134 2 1 -1 1 2.0805
135 2 1 0 1 2.0805
136 2 1 1 1 10.5085
137 2 2 -2 1 11.7812
138 2 2 -1 1 3.3852
139 2 2 0 1 3.3852
140 2 2 1 1 11.7812
141 2 3 -2 1 14.4603
142 2 3 -1 1 6.3372
143 2 3 0 1 6.3372
144 2 3 1 1 14.4603
145 2 4 -2 1 17.8090
146 2 4 -1 1 10.5037
147 2 4 0 1 10.5037
148 2 4 1 1 17.8090
149 2 5 -1 1 15.1709
150 2 5 0 1 15.1709
151 2 -3 -2 2 19.7814
152 2 -3 -1 2 15.6259
153 2 -3 0 2 15.6259
154 2 -3 1 2 19.7814
155 2 -2 -2 2 15.5864
156 2 -2 -1 2 10.6813
157 2 -2 0 2 10.6813
158 2 -2 1 2 15.5864
159 2 -1 -2 2 12.2963
160 2 -1 -1 2 6.3755
161 2 -1 0 2 6.3755
162 2 -1 1 2 12.2963
163 2 0 -3 2 19.8070
164 2 0 -2 2 9.5354
165 2 0 -1 2 4.4893
166 2 0 0 2 4.4893
167 2 0 1 2 9.5354
168 2 0 2 2 19.8070
169 2 1 -3 2 18.9800
170 2 1 -2 2 7.9223
171 2 1 -1 2 1.5608
172 2 1 0 2 1.5608
173 2 1 1 2 7.9223
174 2 1 2 2 18.9800
175 2 2 -3 2 19.6163
176 2 2 -2 2 9.3446
177 2 2 -1 2 2.3977
178 2 2 0 2 2.3977
179 2 2 1 2 9.3446
180 2 2 2 2 19.6163
181 2 3 -2 2 12.9813
182 2 3 -1 2 6.8752
183 2 3 0 2 6.8752
184 2 3 1 2 12.9813
185 2 4 -2 2 16.6867
186 2 4 -1 2 11.6903
187 2 4 0 2 11.6903
188 2 4 1 2 16.6867
189 2 5 -1 2 16.7253
190 2 5 0 2 16.7253
191 2 0 -1 3 19.4475
192 2 0 0 3 19.4475
193 2 1 -1 3 18.1661
194 2 1 0 3 18.1661
195 2 2 -1 3 17.3214
196 2 2 0 3 17.3214
197 2 3 -1 3 17.3918
198 2 3 0 3 17.3918
199 2 4 -1 3 19.0146
200 2 4 0 3 19.0146
THERE ARE ROTATIONS FOR THIS TRANSFORMATION SET
200 Transformations have been processed.


CHARMM> GENErate B DUPLicate A setup
GENPSF> Segment 2 has been generated. Its identifier is B.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 6
Number of atoms = 194 Number of groups = 10
Number of bonds = 194 Number of angles = 210
Number of dihedrals = 322 Number of impropers = 10
Number of cross-terms = 2
Number of HB acceptors = 4 Number of HB donors = 8
Number of NB exclusions = 0 Total charge = 0.00000
Number of Drudes = 30
Number of true-bonds = 97 Number of zero-bonds = 97
Number of aniso. terms = 4 Number of lone-pairs = 10

CHARMM>

CHARMM> open write card name pro_phe_phe_drude.psf unit 32
VOPEN> Attempting to open::pro_phe_phe_drude.psf::
OPNLGU> Unit 32 opened for WRITE access to /home/yuxiang/work/prophephe/crystal/drude/setup/pro_phe_phe_drude.psf

CHARMM> write psf card unit 32
RDTITL> * PSF UNIT CELL
RDTITL> *

CHARMM>

CHARMM> COOR duplicate sele segid A end sele segid B end
SELRPN> 97 atoms have been selected out of 194
SELRPN> 97 atoms have been selected out of 194

CHARMM> coor oper C134 sele segid B end
SELRPN> 97 atoms have been selected out of 194
TRANSFORMATION MATRIX
-1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 -1.000000
4.786499 -5.784450 16.521785
SELECTED COORDINATES TRANSFORMED IN THE MAIN SET.


CHARMM> coor orient norot

ORIENT THE COORDINATES TO ALIGN WITH AXIS

CENTER OF ATOMS BEFORE TRANSLATION 2.39325 3.22998 8.26089
SELECTED COORDINATES TRANSLATED IN THE MAIN SET.
CHARMM> crystal define Monoclinic 5.3214 11.5689 17.0398 90 97.22 90
Crystal Parameters : Crystal Type = MONO
A = 5.32140 B = 11.56890 C = 17.03980
Alpha = 90.00000 Beta = 97.22000 Gamma = 90.00000

CHARMM> crystal build noper 0 cutoff 30
XBUILD> Building all transformations with a minimum atom-atom
contact distance of less than 30.00 Angstroms.

Range of Grid Search for Transformation 1 :
Lattice Vector A -8 TO 8
Lattice Vector B -4 TO 4
Lattice Vector C -3 TO 3


The number of transformations generated = 328


Number Symop A B C Distance

1 1 -6 -1 -2 29.6412
2 1 -6 0 -2 29.6412
3 1 -5 -1 -2 25.4876
4 1 -5 0 -2 25.4876
5 1 -4 -2 -2 26.9405
6 1 -4 -1 -2 21.8465
7 1 -4 0 -2 21.8465
8 1 -4 1 -2 26.9405
9 1 -3 -2 -2 24.3493
10 1 -3 -1 -2 19.0146
11 1 -3 0 -2 19.0146
12 1 -3 1 -2 24.3493
13 1 -2 -3 -2 28.8510
14 1 -2 -2 -2 22.7294
15 1 -2 -1 -2 17.3918
16 1 -2 0 -2 17.3918
17 1 -2 1 -2 22.7294
18 1 -2 2 -2 28.8510
19 1 -1 -3 -2 27.8205
20 1 -1 -2 -2 21.2888
21 1 -1 -1 -2 17.3214
22 1 -1 0 -2 17.3214
23 1 -1 1 -2 21.2888
24 1 -1 2 -2 27.8205
25 1 0 -3 -2 27.6569
26 1 0 -2 -2 20.9570
27 1 0 -1 -2 18.1661
28 1 0 0 -2 18.1661
29 1 0 1 -2 20.9570
30 1 0 2 -2 27.6569
31 1 -6 -2 -1 29.9740
32 1 -6 -1 -1 26.2629
33 1 -6 0 -1 26.8131
34 1 -6 1 -1 28.2613
35 1 -5 -2 -1 25.4604
36 1 -5 -1 -1 21.4173
37 1 -5 0 -1 21.7779
38 1 -5 1 -1 23.9840
39 1 -5 2 -1 28.3050
40 1 -4 -3 -1 28.2539
41 1 -4 -2 -1 21.2762
42 1 -4 -1 -1 16.7253
43 1 -4 0 -1 16.7253
44 1 -4 1 -1 20.1875
45 1 -4 2 -1 24.7010
46 1 -3 -3 -1 24.5727
47 1 -3 -2 -1 17.5026
48 1 -3 -1 -1 11.6903
49 1 -3 0 -1 11.6903
50 1 -3 1 -1 16.6754
51 1 -3 2 -1 21.8087
52 1 -2 -3 -1 21.5868
53 1 -2 -2 -1 12.9813
54 1 -2 -1 -1 6.8752
55 1 -2 0 -1 6.8752
56 1 -2 1 -1 12.6262
57 1 -2 2 -1 19.9433
58 1 -2 3 -1 28.7933
59 1 -1 -3 -1 19.6163
60 1 -1 -2 -1 9.3446
61 1 -1 -1 -1 2.3977
62 1 -1 0 -1 2.3977
63 1 -1 1 -1 9.3446
64 1 -1 2 -1 19.4032
65 1 -1 3 -1 28.4218
66 1 0 -3 -1 18.9800
67 1 0 -2 -1 7.9223
68 1 0 -1 -1 1.5608
69 1 0 0 -1 1.5608
70 1 0 1 -1 7.9223
71 1 0 2 -1 18.8348
72 1 0 3 -1 28.2227
73 1 -6 -1 0 25.8814
74 1 -6 0 0 25.5000
75 1 -6 1 0 25.7993
76 1 -6 2 0 29.0861
77 1 -5 -2 0 25.4615
78 1 -5 -1 0 20.6754
79 1 -5 0 0 20.5455
80 1 -5 1 0 20.9781
81 1 -5 2 0 24.5955
82 1 -4 -2 0 21.2400
83 1 -4 -1 0 15.5478
84 1 -4 0 0 15.6571
85 1 -4 1 0 15.9549
86 1 -4 2 0 20.5064
87 1 -4 3 0 27.0465
88 1 -3 -3 0 26.8107
89 1 -3 -2 0 17.6209
90 1 -3 -1 0 10.6127
91 1 -3 0 0 10.5683
92 1 -3 1 0 10.8976
93 1 -3 2 0 16.6492
94 1 -3 3 0 23.8719
95 1 -2 -3 0 24.0245
96 1 -2 -2 0 14.7386
97 1 -2 -1 0 5.9059
98 1 -2 0 0 5.9051
99 1 -2 1 0 5.9059
100 1 -2 2 0 13.1219
101 1 -2 3 0 21.5605
102 1 -1 -3 0 22.1274
103 1 -1 -2 0 11.7812
104 1 -1 -1 0 2.4304
105 1 -1 0 0 2.4386
106 1 -1 1 0 2.7631
107 1 -1 2 0 11.1268
108 1 -1 3 0 20.4077
109 1 0 -3 0 20.6090
110 1 0 -2 0 10.5085
111 1 0 -1 0 2.5236
112 1 0 1 0 2.5236
113 1 0 2 0 10.5085
114 1 0 3 0 20.6090
115 1 -6 -1 1 28.8273
116 1 -6 0 1 25.9660
117 1 -6 1 1 25.9660
118 1 -6 2 1 29.2908
119 1 -5 -2 1 28.6564
120 1 -5 -1 1 23.9463
121 1 -5 0 1 20.7577
122 1 -5 1 1 20.7577
123 1 -5 2 1 24.4195
124 1 -4 -2 1 24.9045
125 1 -4 -1 1 19.2994
126 1 -4 0 1 15.6259
127 1 -4 1 1 15.6259
128 1 -4 2 1 19.7814
129 1 -4 3 1 27.2796
130 1 -3 -2 1 21.8154
131 1 -3 -1 1 15.1044
132 1 -3 0 1 10.6813
133 1 -3 1 1 10.6813
134 1 -3 2 1 15.5864
135 1 -3 3 1 24.4091
136 1 -2 -3 1 29.6823
137 1 -2 -2 1 19.7033
138 1 -2 -1 1 11.6937
139 1 -2 0 1 6.3755
140 1 -2 1 1 6.3755
141 1 -2 2 1 12.2963
142 1 -2 3 1 21.9324
143 1 -1 -3 1 28.7100
144 1 -1 -2 1 18.6003
145 1 -1 -1 1 9.5354
146 1 -1 0 1 4.4893
147 1 -1 1 1 4.4893
148 1 -1 2 1 9.5354
149 1 -1 3 1 19.8070
150 1 0 -3 1 28.2227
151 1 0 -2 1 18.8348
152 1 0 -1 1 7.9223
153 1 0 0 1 1.5608
154 1 0 1 1 1.5608
155 1 0 2 1 7.9223
156 1 0 3 1 18.9800
157 1 -4 0 2 26.6130
158 1 -4 1 2 26.6130
159 1 -3 -1 2 26.8944
160 1 -3 0 2 23.5665
161 1 -3 1 2 23.5665
162 1 -3 2 2 26.8944
163 1 -2 -2 2 29.9612
164 1 -2 -1 2 23.9159
165 1 -2 0 2 21.4277
166 1 -2 1 2 21.4277
167 1 -2 2 2 23.9159
168 1 -2 3 2 29.9612
169 1 -1 -2 2 28.3368
170 1 -1 -1 2 21.8464
171 1 -1 0 2 19.4475
172 1 -1 1 2 19.4475
173 1 -1 2 2 21.8464
174 1 -1 3 2 28.3368
175 1 0 -2 2 27.6569
176 1 0 -1 2 20.9570
177 1 0 0 2 18.1661
178 1 0 1 2 18.1661
179 1 0 2 2 20.9570
180 1 0 3 2 27.6569
181 1 6 1 2 29.6412
182 1 6 0 2 29.6412
183 1 5 1 2 25.4876
184 1 5 0 2 25.4876
185 1 4 2 2 26.9405
186 1 4 1 2 21.8465
187 1 4 0 2 21.8465
188 1 4 -1 2 26.9405
189 1 3 2 2 24.3493
190 1 3 1 2 19.0146
191 1 3 0 2 19.0146
192 1 3 -1 2 24.3493
193 1 2 3 2 28.8510
194 1 2 2 2 22.7294
195 1 2 1 2 17.3918
196 1 2 0 2 17.3918
197 1 2 -1 2 22.7294
198 1 2 -2 2 28.8510
199 1 1 3 2 27.8205
200 1 1 2 2 21.2888
201 1 1 1 2 17.3214
202 1 1 0 2 17.3214
203 1 1 -1 2 21.2888
204 1 1 -2 2 27.8205
205 1 6 2 1 29.9740
206 1 6 1 1 26.2629
207 1 6 0 1 26.8131
208 1 6 -1 1 28.2613
209 1 5 2 1 25.4604
210 1 5 1 1 21.4173
211 1 5 0 1 21.7779
212 1 5 -1 1 23.9840
213 1 5 -2 1 28.3050
214 1 4 3 1 28.2539
215 1 4 2 1 21.2762
216 1 4 1 1 16.7253
217 1 4 0 1 16.7253
218 1 4 -1 1 20.1875
219 1 4 -2 1 24.7010
220 1 3 3 1 24.5727
221 1 3 2 1 17.5026
222 1 3 1 1 11.6903
223 1 3 0 1 11.6903
224 1 3 -1 1 16.6754
225 1 3 -2 1 21.8087
226 1 2 3 1 21.5868
227 1 2 2 1 12.9813
228 1 2 1 1 6.8752
229 1 2 0 1 6.8752
230 1 2 -1 1 12.6262
231 1 2 -2 1 19.9433
232 1 2 -3 1 28.7933
233 1 1 3 1 19.6163
234 1 1 2 1 9.3446
235 1 1 1 1 2.3977
236 1 1 0 1 2.3977
237 1 1 -1 1 9.3446
238 1 1 -2 1 19.4032
239 1 1 -3 1 28.4218
240 1 6 1 0 25.8814
241 1 6 0 0 25.5000
242 1 6 -1 0 25.7993
243 1 6 -2 0 29.0861
244 1 5 2 0 25.4615
245 1 5 1 0 20.6754
246 1 5 0 0 20.5455
247 1 5 -1 0 20.9781
248 1 5 -2 0 24.5955
249 1 4 2 0 21.2400
250 1 4 1 0 15.5478
251 1 4 0 0 15.6571
252 1 4 -1 0 15.9549
253 1 4 -2 0 20.5064
254 1 4 -3 0 27.0465
255 1 3 3 0 26.8107
256 1 3 2 0 17.6209
257 1 3 1 0 10.6127
258 1 3 0 0 10.5683
259 1 3 -1 0 10.8976
260 1 3 -2 0 16.6492
261 1 3 -3 0 23.8719
262 1 2 3 0 24.0245
263 1 2 2 0 14.7386
264 1 2 1 0 5.9059
265 1 2 0 0 5.9051
266 1 2 -1 0 5.9059
267 1 2 -2 0 13.1219
268 1 2 -3 0 21.5605
269 1 1 3 0 22.1274
270 1 1 2 0 11.7812
271 1 1 1 0 2.4304
272 1 1 0 0 2.4386
273 1 1 -1 0 2.7631
274 1 1 -2 0 11.1268
275 1 1 -3 0 20.4077
276 1 6 1 -1 28.8273
277 1 6 0 -1 25.9660
278 1 6 -1 -1 25.9660
279 1 6 -2 -1 29.2908
280 1 5 2 -1 28.6564
281 1 5 1 -1 23.9463
282 1 5 0 -1 20.7577
283 1 5 -1 -1 20.7577
284 1 5 -2 -1 24.4195
285 1 4 2 -1 24.9045
286 1 4 1 -1 19.2994
287 1 4 0 -1 15.6259
288 1 4 -1 -1 15.6259
289 1 4 -2 -1 19.7814
290 1 4 -3 -1 27.2796
291 1 3 2 -1 21.8154
292 1 3 1 -1 15.1044
293 1 3 0 -1 10.6813
294 1 3 -1 -1 10.6813
295 1 3 -2 -1 15.5864
296 1 3 -3 -1 24.4091
297 1 2 3 -1 29.6823
298 1 2 2 -1 19.7033
299 1 2 1 -1 11.6937
300 1 2 0 -1 6.3755
301 1 2 -1 -1 6.3755
302 1 2 -2 -1 12.2963
303 1 2 -3 -1 21.9324
304 1 1 3 -1 28.7100
305 1 1 2 -1 18.6003
306 1 1 1 -1 9.5354
307 1 1 0 -1 4.4893
308 1 1 -1 -1 4.4893
309 1 1 -2 -1 9.5354
310 1 1 -3 -1 19.8070
311 1 4 0 -2 26.6130
312 1 4 -1 -2 26.6130
313 1 3 1 -2 26.8944
314 1 3 0 -2 23.5665
315 1 3 -1 -2 23.5665
316 1 3 -2 -2 26.8944
317 1 2 2 -2 29.9612
318 1 2 1 -2 23.9159
319 1 2 0 -2 21.4277
320 1 2 -1 -2 21.4277
321 1 2 -2 -2 23.9159
322 1 2 -3 -2 29.9612
323 1 1 2 -2 28.3368
324 1 1 1 -2 21.8464
325 1 1 0 -2 19.4475
326 1 1 -1 -2 19.4475
327 1 1 -2 -2 21.8464
328 1 1 -3 -2 28.3368
THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET
328 Transformations have been processed.


CHARMM> !(-X, Y+1/2,-Z)
CHARMM>

CHARMM> image BYSEgments xcen 0.0 ycen 0.0 zcen 0.0 select all end
SELRPN> 194 atoms have been selected out of 194
IMAGE CENTERING ON FOR SOME ATOMS

CHARMM> !update inbfrq -1 imgfrq -1 ihbfrq 0 -
CHARMM> !ewald pmewald kappa 0.34 fftx 64 ffty 64 fftz 64 order 6 lrc -
CHARMM> !@eatom @etrun @vatom @vtrun cutnb @cutnb ctonnb @ctonnb ctofnb @ctofnb -
CHARMM> !cutim @cutim
CHARMM>

CHARMM> nbonds atom vatom switch vswitch bycb -
CHARMM> ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 LRC -
CHARMM> inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
CHARMM> ewald pmew fftx 64 ffty 64 fftz 64 kappa .34 spline order 6

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000

: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included

Total heap storage needed = 291775
Fill Ewald table: Number of points= 10000 EWXmax= 4.250000
fill erfc table: linear inter has rms error = 0.979220D-08 maximum error = 0.218740D-07
fill erfc table: cubic spline has rms error = 0.360331D-11 maximum error = 0.108438D-10

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
1753 1753 1746
: Ran out of space. RESIZING
with mode 5 found 1144 exclusions and 802 interactions(1-4)
found 14 group exclusions.
found 0 image group exclusions.
Generating nonbond list with Exclusion mode = 5
Allocate space for 5000 Thole shielding pairs
== PRIMARY == SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS

=========================================
TRIAL run of list...........
=========================================
Using Image CUBE search
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs

CHARMM>

CHARMM> ener

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000

: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included

found 0 image group exclusions.

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 16918 atom pairs and 1946 atom exclusions.
There are 0 group pairs and 14 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 21993 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 379810 ATOM PAIRS AND 0 GROUP PAIRS
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
ENER LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
ENER> 0 NaN 0.00000 NaN
ENER INTERN> 291.17021 68.74474 60.35920 83.68291 0.03064
ENER CROSS> -10.14152 0.00000 0.00000 0.00000
ENER EXTERN> 200.16780 NaN 0.00000 0.00000 0.00000
ENER IMAGES> 324.20643 -62.58982 0.00000 0.00000 0.00000
ENER EWALD> 23.24862 -31944.61258 31862.78470 0.00000 0.00000
ENER LRCor> -2.16473 -4.32864
---------- --------- --------- --------- --------- ---------

CHARMM>

CHARMM> ! minimization
CHARMM>

CHARMM> cons harm force 100000. sele .not. type D* end
SELRPN> 134 atoms have been selected out of 194
CSTRAN: Harmonic Restraints
ABSOlute type as set number 1. Number of selected atoms: 134
Reference coordinates set to main coordinates.
Mass weighting will NOT be used for new restraints.
The force constant of 100000.00000 will be used.
An exponent of 2 will be used.
The XYZ scale factors are: 1.00000 1.00000 1.00000
A total of 134 atoms are restrained.

CHARMM> mini ABNR nstep 1000 nprint 20

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000

: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
1 C001 has 0 0 0 28.06
2 C002 has 0 0 0 28.06
3 C003 has 0 0 0 23.89
4 C004 has 0 0 0 23.89
5 C005 has 0 0 0 21.39
6 C006 has 0 0 0 20.26
7 C007 has 0 0 0 20.26
8 C008 has 0 0 0 21.54
9 C009 has 0 0 0 18.82
10 C010 has 0 0 0 17.52
11 C011 has 0 0 0 17.52
12 C012 has 0 0 0 18.99
13 C013 has 0 0 0 24.49
14 C014 has 0 0 0 17.53
15 C015 has 0 0 0 16.13
16 C016 has 0 0 0 16.13
17 C017 has 0 0 0 17.72
18 C018 has 0 0 0 21.88
19 C019 has 0 0 0 24.61
20 C020 has 0 0 0 17.69
21 C021 has 0 0 0 16.30
22 C022 has 0 0 0 16.30
23 C023 has 0 0 0 17.66
24 C024 has 0 0 0 21.69
25 C025 has 0 0 0 24.95
26 C026 has 0 0 0 18.16
27 C027 has 0 0 0 16.81
28 C028 has 0 0 0 16.81
29 C029 has 0 0 0 18.17
30 C030 has 0 0 0 22.11
31 C031 has 0 0 0 25.89
32 C032 has 0 0 0 24.35
33 C033 has 0 0 0 24.35
34 C034 has 0 0 0 24.91
35 C035 has 0 0 0 20.83
36 C036 has 0 0 0 19.29
37 C037 has 0 0 0 19.29
38 C038 has 0 0 0 19.99
39 C039 has 0 0 0 22.15
40 C040 has 0 0 0 23.37
41 C041 has 0 0 0 15.93
42 C042 has 30 1 1 14.37
43 C043 has 55 2 2 14.37
44 C044 has 0 0 0 15.34
45 C045 has 0 0 0 18.25
46 C046 has 0 0 0 20.55
47 C047 has 30 1 1 11.38
48 C048 has 122 6 4 9.08
49 C049 has 194 10 6 9.08
50 C050 has 118 6 4 10.92
51 C051 has 0 0 0 15.24
52 C052 has 0 0 0 18.82
53 C053 has 97 5 3 7.84
54 C054 has 194 10 6 3.78
55 C055 has 194 10 6 3.78
56 C056 has 194 10 6 5.67
57 C057 has 0 0 0 13.16
58 C058 has 0 0 0 21.92
59 C059 has 0 0 0 18.43
60 C060 has 97 5 3 6.86
61 C061 has 194 10 6 0.00
62 C062 has 194 10 6 0.00
63 C063 has 194 10 6 1.26
64 C064 has 0 0 0 12.11
65 C065 has 0 0 0 22.04
66 C066 has 0 0 0 18.43
67 C067 has 97 5 3 6.86
68 C068 has 194 10 6 0.00
69 C069 has 194 10 6 0.00
70 C070 has 194 10 6 1.54
71 C071 has 0 0 0 12.33
72 C072 has 0 0 0 22.33
73 C073 has 0 0 0 24.47
74 C074 has 0 0 0 24.32
75 C075 has 0 0 0 24.32
76 C076 has 0 0 0 25.27
77 C077 has 0 0 0 21.32
78 C078 has 0 0 0 19.17
79 C079 has 0 0 0 19.02
80 C080 has 0 0 0 19.02
81 C081 has 0 0 0 20.22
82 C082 has 0 0 0 16.39
83 C083 has 55 2 2 13.87
84 C084 has 139 7 5 13.73
85 C085 has 22 1 1 13.73
86 C086 has 0 0 0 15.35
87 C087 has 0 0 0 22.98
88 C088 has 0 0 0 20.78
89 C089 has 55 2 2 11.79
90 C090 has 194 10 6 8.58
91 C091 has 194 10 6 8.43
92 C092 has 194 10 6 8.43
93 C093 has 34 2 1 10.87
94 C094 has 0 0 0 20.27
95 C095 has 0 0 0 18.93
96 C096 has 105 5 4 8.09
97 C097 has 194 10 6 3.28
98 C098 has 194 10 6 3.13
99 C099 has 194 10 6 3.13
100 C100 has 119 6 4 7.55
101 C101 has 0 0 0 18.70
102 C102 has 0 0 0 18.43
103 C103 has 135 7 4 6.86
104 C104 has 194 10 6 0.00
105 C105 has 194 10 6 0.00
106 C106 has 194 10 6 0.00
107 C107 has 119 6 4 6.86
108 C108 has 0 0 0 18.43
109 C109 has 0 0 0 18.43
110 C110 has 160 8 5 6.86
111 C111 has 194 10 6 0.00
115 C115 has 0 0 0 26.12
116 C116 has 0 0 0 25.18
117 C117 has 0 0 0 25.18
118 C118 has 0 0 0 26.10
119 C119 has 0 0 0 23.27
120 C120 has 0 0 0 21.05
121 C121 has 0 0 0 19.87
122 C122 has 0 0 0 19.87
123 C123 has 0 0 0 21.03
124 C124 has 0 0 0 18.79
125 C125 has 0 0 0 16.03
126 C126 has 22 1 1 14.58
127 C127 has 22 1 1 14.58
128 C128 has 0 0 0 16.12
129 C129 has 0 0 0 23.50
130 C130 has 0 0 0 14.88
131 C131 has 63 3 2 10.72
132 C132 has 122 6 4 9.32
133 C133 has 97 5 3 9.32
134 C134 has 22 1 1 11.58
135 C135 has 0 0 0 20.66
136 C136 has 0 0 0 22.36
137 C137 has 0 0 0 12.10
138 C138 has 172 9 6 5.46
139 C139 has 194 10 6 4.22
140 C140 has 186 9 6 4.22
141 C141 has 64 3 2 8.06
142 C142 has 0 0 0 18.91
143 C143 has 0 0 0 21.80
144 C144 has 0 0 0 11.21
145 C145 has 172 9 6 1.12
146 C146 has 194 10 6 0.29
147 C147 has 194 10 6 1.57
148 C148 has 97 5 3 7.05
149 C149 has 0 0 0 18.50
157 C157 has 0 0 0 24.99
158 C158 has 0 0 0 24.99
159 C159 has 0 0 0 21.47
160 C160 has 0 0 0 21.44
161 C161 has 0 0 0 21.50
162 C162 has 0 0 0 22.87
163 C163 has 0 0 0 22.62
164 C164 has 0 0 0 18.79
165 C165 has 0 0 0 18.75
166 C166 has 0 0 0 18.82
167 C167 has 0 0 0 20.77
168 C168 has 0 0 0 26.91
169 C169 has 0 0 0 21.46
170 C170 has 0 0 0 17.37
171 C171 has 0 0 0 17.33
172 C172 has 0 0 0 17.40
173 C173 has 0 0 0 19.87
174 C174 has 0 0 0 26.22
Total of 7284 atoms and 369 groups and 232 residues were included

found 0 image group exclusions.

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYCB NOEXtnd EWALd
CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6
FFTX= 64 FFTY= 64 FFTZ= 64
Using Pub FFT
Real-to-Complex FFT
There are 16918 atom pairs and 1946 atom exclusions.
There are 0 group pairs and 14 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 21993 ATOM PAIRS AND 0 GROUP PAIRS
== IMAGES === SPACE FOR 379810 ATOM PAIRS AND 0 GROUP PAIRS
Using Image CUBE search
NBNDGCM found:
16918 atom pairs
292162 image atom pairs
0 self atom pairs
16918 total atom pairs
292162 total image pairs


ABNER> An energy minimization has been requested.

EIGRNG = 0.0005000 MINDIM = 5
NPRINT = 20 NSTEP = 1000
PSTRCT = 0.0000000 SDSTP = 0.0200000
STPLIM = 1.0000000 STRICT = 0.1000000
TOLFUN = 0.0000000 TOLGRD = 0.0000000
TOLITR = 100 TOLSTP = 0.0000000
FMEM = 0.0000000
MINI MIN: Cycle ENERgy Delta-E GRMS Step-size
MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MINI CROSS: CMAPs PMF1D PMF2D PRIMO
MINI EXTERN: VDWaals ELEC HBONds ASP USER
MINI IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MINI EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MINI LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MINI> 0 NaN NaN NaN 0.00000
MINI INTERN> 291.17021 68.74474 60.35920 83.68291 0.03064
MINI CROSS> -10.14152 0.00000 0.00000 0.00000
MINI EXTERN> 200.16780 NaN 0.00000 0.00000 0.00000
MINI IMAGES> 324.20643 -62.58982 0.00000 0.00000 0.00000
MINI EWALD> 23.24862 -31944.61258 31862.78470 0.00000 0.00000
MINI LRCor> -2.16473 -4.32864
---------- --------- --------- --------- --------- ---------
UPDECI: Image update at step 1

: updating the image atom lists and remapping
Transformation Atoms Groups Residues Min-Distance
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[4774,1],0]
Exit code: 174
--------------------------------------------------------------------------
Posted By: rmv Re: Infinte ELEC energy of Drude simulation - 04/12/21 03:53 PM
Please refer to the READ BEFORE POSTING topic for helpful hints, esp. for the use of .txt file attachments.

One possibility is a problem with the Drude conversion, or the initial relaxation of the Drude particles.
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