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ardie Offline OP
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Dear all,
I want to build hydrogen atoms to the center carbon atom of methane. But I get the following error message and can't remove it. Can you give me some suggestion? Thanks.

1. Here is methane toppology file:
******************************************************************************************************
RESI METH 0.00 !
GROUP
ATOM C1 CT3 -0.36 !
ATOM H11 HA 0.09 !
ATOM H12 HA 0.09 !
ATOM H13 HA 0.09 !
ATOM H14 HA 0.09 !

BOND C1 H11 C1 H12 C1 H13 C1 H14
!ANGLE H11 C1 H12 H11 C1 H13 H11 C1 H14
!ANGLE H12 C1 H13 H12 C1 H14 H13 C1 H14
PATCHING FIRS NONE LAST NONE

IC BLNK H11 C1 H14 0.0000 0.0000 60.0000 0.0000 0.0000
IC H13 H11 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000
IC H14 H11 *C1 H13 0.0000 0.0000 120.0000 0.0000 0.0000
IC H12 H13 *C1 H11 0.0000 0.0000 120.0000 0.0000 0.0000

END

******************************************************************************************************

2. here is my input script:
***************************************
* charmm input
*

BOMLEV -2

! Topology files
open read unit 1 card name ./lib/top_all22_prot.inp
read rtf card unit 1
close unit 1

open read unit 1 card name ./lib/meth_my.top
read rtf card append unit 1
close unit 1

! Parameter files
open read unit 2 card name ./lib/par_all.inp
read para card unit 2
close unit 2

! Read substrate methane
open read unit 10 card name ./coor/meth1.pdb
read sequence pdb unit 10
generate METH warn setup
rewind unit 10
read coor pdb resi unit 10
close unit 10

ic fill preserve
ic parameters
ic build
hbuild

! Write full structure and the corresponding psf file
open write unit 30 card name ./out/meth2.pdb
write coor pdb unit 30
* CH4
*
close unit 30


open write unit 30 card name ./out/meth2.crd
write coor card unit 30
* CH4
*

open write unit 40 card name ./out/meth2.psf
write psf card unit 40
* CH4
*
close unit 40

stop
***************************************

3. here is the output error:
******************
CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"

CHARMM>

CHARMM> ic fill preserve

CHARMM> ic parameters

CHARMM> ic build

***** LEVEL 1 WARNING FROM <BUILDC> *****
***** SOME COORDINATES NOT BUILT
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

**** WARNING **** 4 COORDINATES ARE STILL UNDEFINED

CHARMM> hbuild
PRNHBD: CUToff Hydrogen Bond distance = 0.5000 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 SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
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.
<MAKINB> with mode 5 found 10 exclusions and 0 interactions(1-4)
<MAKGRP> found 0 group exclusions.

CUToff Hydrogen Bond distance = 0.5000 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= 7.5000

ERROR FROM HBUILD: missing lone pairs for METH 1 METH
*** LEVEL 0 WARNING *** BOMLEV IS -2
Place:H11 ,H12 ,H13 ,H14 constructed for water METH 1 METH C1 .

CHARMM>

******************************


You can see from the last line, the output said: Place:H11 ,H12 ,H13 ,H14 constructed for water METH 1 METH C1 .

I don't know why METH is recognized as water?



4. here is input coordinate file meth1.pdb

ATOM 1 C1 METH 1 4.857 -0.573 -2.095 1.00 0.00 METH
END

5. here is output meth2.pdb
ATOM 1 C1 METH 1 4.857 -0.573 -2.095 1.00 0.00 METH
ATOM 2 H11 METH 1 4.857 0.538 -2.095 1.00 0.00 METH
ATOM 3 H12 METH 1 4.857 -0.924 -3.149 1.00 0.00 METH
ATOM 4 H13 METH 1 9999.0009999.0009999.000 1.00 0.00 METH
ATOM 5 H14 METH 1 9999.0009999.0009999.000 1.00 0.00 METH
TER 6 METH 1
END



************************
Ardie

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google "methane coordinates" gives:
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000

I don't know why your script didn't work, but here is a more compact form of it (easier to read, less error prone):
* charmm input
*
! Topology files
read rtf card name ./lib/top_all22_prot.inp
read rtf card append name ./lib/meth_my.top
! Parameter files
read para card name ./lib/par_all.inp
! Read substrate methane
read sequence meth 1
generate METH warn setup
read coor pdb resi name name ./coor/meth1.pdb
ic parameters
ic build
hbuild

! Write full structure and the corresponding psf file
write coor pdb name ./out/meth2.pdb
* CH4
*
write coor card name ./out/meth2.crd
* CH4
*
write psf card name ./out/meth2.psf
* CH4
*
stop


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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ardie Offline OP
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Originally Posted By: lennart
google "methane coordinates" gives:
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000

I don't know why your script didn't work, but here is a more compact form of it (easier to read, less error prone):
* charmm input
*
! Topology files
read rtf card name ./lib/top_all22_prot.inp
read rtf card append name ./lib/meth_my.top
! Parameter files
read para card name ./lib/par_all.inp
! Read substrate methane
read sequence meth 1
generate METH warn setup
read coor pdb resi name name ./coor/meth1.pdb
ic parameters
ic build
hbuild

! Write full structure and the corresponding psf file
write coor pdb name ./out/meth2.pdb
* CH4
*
write coor card name ./out/meth2.crd
* CH4
*
write psf card name ./out/meth2.psf
* CH4
*
stop


Hi Lennart,
Thanks. I took your script to run again. Now this time the error message is different from last time by my script.
Here is the output:


CHARMM> read sequence meth 1

CHARMM> generate METH warn setup
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
GENPSF> Segment 1 has been generated. Its identifier is METH.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues = 1
Number of atoms = 5 Number of groups = 1
Number of bonds = 4 Number of angles = 6
Number of dihedrals = 0 Number of impropers = 0
Number of cross-terms = 0
Number of HB acceptors = 0 Number of HB donors = 0
Number of NB exclusions = 0 Total charge = 0.00000

CHARMM> !read coor pdb resi name name ./coor/meth.pdb
CHARMM> read coor pdb resi name ./coor/meth.pdb
VOPEN> Attempting to open::./coor/meth.pdb::
read CHARMM-pdb format
SPATIAL COORDINATES BEING READ FROM UNIT 90
TITLE> *
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 METH H11
** WARNING ** After reading, there are no coordinates for selected atom: 3 1 METH H12
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 METH H13
** WARNING ** After reading, there are no coordinates for selected atom: 5 1 METH H14

** A total of 4 selected atoms have no coordinates
*** LEVEL 2 WARNING *** BOMLEV IS 0
VCLOSE: Closing unit 90 with status "KEEP"

CHARMM> ic parameters

CHARMM> ic build

***** LEVEL 1 WARNING FROM <BUILDC> *****
***** SOME COORDINATES NOT BUILT
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

**** WARNING **** 4 COORDINATES ARE STILL UNDEFINED

CHARMM> hbuild
PRNHBD: CUToff Hydrogen Bond distance = 0.5000 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 SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
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.
<MAKINB> with mode 5 found 10 exclusions and 0 interactions(1-4)
<MAKGRP> found 0 group exclusions.

CUToff Hydrogen Bond distance = 0.5000 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= 7.5000

ERROR FROM HBUILD: missing lone pairs for METH 1 METH
*** LEVEL 0 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.


/---------\
/ \
/ \
/ \
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
--\ XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
\ /
-- --
\---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX
XXXXX
XXX XXX
XXX XXX
XXX XXX
XXXXX XXXXX
XXXX XXXX
XXX XXX




I doubt my written methan toppology and parameter file may not correct. But I can't find out where is the problem.


Ardie

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rmv Online Content
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If you want to read the H atom coords, they must have the same names as in the residue description, i.e. H11, etc.

IC BUILD requires that at least 3 bonded atoms have coordinates.

The "missing lone pairs" error message does suggest a problem with HBUILD in some way.

If you read the H atom coords from a file, then you don't really need IC BUILD or HBUILD.


Rick Venable
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ardie Offline OP
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Originally Posted By: rmv
If you want to read the H atom coords, they must have the same names as in the residue description, i.e. H11, etc.

IC BUILD requires that at least 3 bonded atoms have coordinates.

The "missing lone pairs" error message does suggest a problem with HBUILD in some way.

If you read the H atom coords from a file, then you don't really need IC BUILD or HBUILD.

Hi Rick,
Then do you think the toppology file written by me is fine or not?

Ardie

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I usually let CHARMM tell me that ...


Rick Venable
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ardie Offline OP
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Originally Posted By: rmv
I usually let CHARMM tell me that ...

OK, Thanks.

Now I provide the H atoms' coordinates, no warning messagen then.


Ardie

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I feel this thread belongs in the "Setup, I/O, and Basic questions" forum.

There are multiple ways to solve the problem, depending on "the bigger picture". If many methane molecules are needed, one could first generate one around the origin (for instance by using IC SEED or the coordinates Googled by Lennart), then generate many copies, each of them translated to their respective target positions; see attached me1.inp for a proof of concept. If only one copy is needed, the easiest way is to just craft a pdb file with all atoms at the right positions (and with the right atom names). The way you were trying to do it is the most complicated (but nothing's impossible; see attached me2.inp ).

And then people say nothing is easy with CHARMM. crazy

Attached Images
me1.inp.txt (910 Bytes, 691 downloads)
me2.inp.txt (1.29 KB, 583 downloads)

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