Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
Joined: Oct 2022
Posts: 10
J
Forum Member
OP Offline
Forum Member
J
Joined: Oct 2022
Posts: 10
Hello all, for the above topic I generated a fix.str file while generating a ligand topology within CGenFF beneath the Gromacs Protein-Ligand Complex Tutorial.
My resulting .str file exhibited penalties over 50 for two-dihedral angles which I could not discover how to read i.e. which atoms/angles within my ligand? The
file exhibiting these penalties is below:

OG311 CG2O2 CG2R51 CG2R51 0.0369 2 180.00 ! 14C+H , from CG2DC1 CG2O5 CG2R51 CG2R51, penalty= 74.5
OG311 CG2O2 CG2R51 NG2R51 1.5853 2 180.00 ! 14C+H , from CG2DC1 CG2O5 CG2R51 NG2R51, penalty= 74.5

and my previously generated fixmol.2 is exhibited below:

@MOLECULE
14C+H
66 70 0 0 0
SMALL
USER_CHARGES

@ATOM
1 N 111.3820 109.6340 61.8800 N.ar 1 14C+H -0.3303
2 N 105.4060 107.0540 60.4920 N.3 1 14C+H -0.1680
3 C 110.1840 109.4550 61.1970 C.ar 1 14C+H 0.0501
4 C 109.3410 108.7420 62.0460 C.ar 1 14C+H 0.0025
5 C 107.5970 108.8580 60.3650 C.ar 1 14C+H 0.1062
6 C 108.0360 108.4370 61.6280 C.ar 1 14C+H -0.0262
7 C 111.3520 108.9490 63.0940 C.ar 1 14C+H 0.1281
8 C 112.5320 110.3770 61.3510 C.3 1 14C+H 0.0491
9 C 110.0630 108.4580 63.2300 C.ar 1 14C+H -0.0220
10 C 109.7560 109.8640 59.9170 C.ar 1 14C+H -0.0357
11 C 104.5350 106.7890 61.6470 C.3 1 14C+H 0.0459
12 C 105.5700 105.9440 59.5060 C.3 1 14C+H 0.0459
13 C 108.4390 109.5800 59.5230 C.ar 1 14C+H -0.0334
14 C 113.2790 109.7190 60.2020 C.ar 1 14C+H -0.0277
15 C 103.6320 105.5790 61.6370 C.ar 1 14C+H -0.0317
16 C 106.6830 104.9750 59.8460 C.ar 1 14C+H -0.0317
17 C 112.4800 108.8090 63.9960 C.2 1 14C+H 0.3535
18 C 113.1040 108.3390 59.9930 C.ar 1 14C+H -0.0561
19 C 114.2410 110.3690 59.4190 C.ar 1 14C+H -0.0561
20 C 102.7730 105.2960 60.5710 C.ar 1 14C+H -0.0573
21 C 108.0190 105.3870 59.8010 C.ar 1 14C+H -0.0573
22 C 103.6260 104.7120 62.7470 C.ar 1 14C+H -0.0573
23 C 106.4080 103.6190 60.0630 C.ar 1 14C+H -0.0573
24 C 113.8850 107.6310 59.0650 C.ar 1 14C+H -0.0475
25 C 115.0390 109.6620 58.5130 C.ar 1 14C+H -0.0475
26 C 114.8860 108.2840 58.3390 C.ar 1 14C+H 0.0589
27 C 101.9850 104.1420 60.5780 C.ar 1 14C+H -0.0615
28 C 109.0560 104.4560 59.8080 C.ar 1 14C+H -0.0615
29 C 102.8380 103.5590 62.7530 C.ar 1 14C+H -0.0615
30 C 107.4460 102.6850 60.0880 C.ar 1 14C+H -0.0615
31 C 102.0260 103.2680 61.6610 C.ar 1 14C+H -0.0617
32 C 108.7650 103.1000 59.9240 C.ar 1 14C+H -0.0617
33 C 115.8290 107.6190 57.3880 C.2 1 14C+H 0.3368
34 O 105.1310 109.5650 60.6820 O.2 1 14C+H -0.1528
35 O 105.8280 108.5390 58.5070 O.2 1 14C+H -0.1528
36 O 112.1810 108.0590 65.0840 O.3 1 14C+H -0.4761
37 O 113.5750 109.3310 63.8560 O.2 1 14C+H -0.2435
38 O 115.7970 106.2720 57.3580 O.3 1 14C+H -0.4771
39 O 116.5990 108.2550 56.6850 O.2 1 14C+H -0.2451
40 S 105.8890 108.5700 59.9540 S.O2 1 14C+H 0.0614
41 H 112.8860 108.0370 65.7540 H 1 14C+H 0.2955
42 H 114.9270 105.8510 57.2880 H 1 14C+H 0.2954
43 H 107.4035 107.9060 62.2469 H 1 14C+H 0.0644
44 H 113.2258 110.5209 62.1528 H 1 14C+H 0.0541
45 H 112.1301 111.2847 60.9517 H 1 14C+H 0.0541
46 H 109.6911 107.9665 64.0577 H 1 14C+H 0.0647
47 H 110.3988 110.3626 59.2821 H 1 14C+H 0.0639
48 H 103.9052 107.6460 61.7646 H 1 14C+H 0.0493
49 H 105.2245 106.5806 62.4382 H 1 14C+H 0.0493
50 H 105.7789 106.3732 58.5484 H 1 14C+H 0.0493
51 H 104.6585 105.3836 59.5175 H 1 14C+H 0.0493
52 H 108.0939 109.9071 58.6071 H 1 14C+H 0.0638
53 H 112.3846 107.8348 60.5345 H 1 14C+H 0.0621
54 H 114.3637 111.3894 59.5121 H 1 14C+H 0.0621
55 H 102.7203 105.9458 59.7710 H 1 14C+H 0.0621
56 H 108.2398 106.3943 59.7621 H 1 14C+H 0.0621
57 H 104.2122 104.9319 63.5674 H 1 14C+H 0.0621
58 H 105.4341 103.3086 60.2050 H 1 14C+H 0.0621
59 H 113.7192 106.6231 58.9180 H 1 14C+H 0.0626
60 H 115.7525 110.1666 57.9641 H 1 14C+H 0.0626
61 H 101.3691 103.9364 59.7758 H 1 14C+H 0.0618
62 H 110.0355 104.7708 59.7275 H 1 14C+H 0.0618
63 H 102.8579 102.9237 63.5661 H 1 14C+H 0.0618
64 H 107.2349 101.6846 60.2284 H 1 14C+H 0.0618
65 H 101.4563 102.4075 61.6539 H 1 14C+H 0.0618
66 H 109.5255 102.4033 59.8885 H 1 14C+H 0.0618
@BOND
1 1 3 ar
2 1 7 ar
3 1 8 1
4 2 11 1
5 2 12 1
6 2 40 1
7 3 4 ar
8 3 10 ar
9 4 6 ar
10 4 9 ar
11 5 6 ar
12 5 13 ar
13 5 40 1
14 6 43 1
15 7 9 ar
16 7 17 1
17 8 14 1
18 8 44 1
19 8 45 1
20 9 46 1
21 10 13 ar
22 10 47 1
23 11 15 1
24 11 48 1
25 11 49 1
26 12 16 1
27 12 50 1
28 12 51 1
29 13 52 1
30 14 18 ar
31 14 19 ar
32 15 20 ar
33 15 22 ar
34 16 21 ar
35 16 23 ar
36 17 36 1
37 17 37 2
38 18 24 ar
39 18 53 1
40 19 25 ar
41 19 54 1
42 20 27 ar
43 20 55 1
44 21 28 ar
45 21 56 1
46 22 29 ar
47 22 57 1
48 23 30 ar
49 23 58 1
50 24 26 ar
51 24 59 1
52 25 26 ar
53 25 60 1
54 26 33 1
55 27 31 ar
56 27 61 1
57 28 32 ar
58 28 62 1
59 29 31 ar
60 29 63 1
61 30 32 ar
62 30 64 1
63 31 65 1
64 32 66 1
65 33 38 1
66 33 39 2
67 34 40 2
68 35 40 2
69 36 41 1
70 38 42 1

Joined: Sep 2003
Posts: 8,650
Likes: 26
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,650
Likes: 26
Two things--
  • This a CHARMM site, so for GROMACS help you will have to look elsewhere.
  • If these issues arise from charmm-gui, that is an independent web site with their own support mechanism.


End of line.


Rick Venable
computational chemist

Joined: Oct 2022
Posts: 10
J
Forum Member
OP Offline
Forum Member
J
Joined: Oct 2022
Posts: 10
Hi Rick thank you for your kind update and this actually happened via CGenFF, accordingly if you know where I should then properly inquire abour CGenFF Topics feel free to update me accordingly.

Thanks:)

Last edited by Joel Subach; 01/31/23 05:36 PM.
Joined: Sep 2003
Posts: 4,881
Likes: 12
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,881
Likes: 12
OG311 CG2O2 CG2R51 CG2R51 are the atom TYPEs for the four atoms involved in the dihedral, not the NAMES. You have to check the RESIdue definition to find the connected atoms that have been assinge hese types


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Oct 2022
Posts: 10
J
Forum Member
OP Offline
Forum Member
J
Joined: Oct 2022
Posts: 10
Hi Lennart thank you for your kind update:).

What do the later signify i.e. from CG2DC1 CG2O5 CG2R51 CG2R51, penalty= 74.5?

Thanks:)

Joined: Sep 2003
Posts: 4,881
Likes: 12
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,881
Likes: 12
Huh?
OG311 CG2O2 CG2R51 CG2R51 are the four atom types involved in the dihedral
0.0369 2 180.00 are the "force constant", multiplicity and phase angle of this particular energy term. Please consult your supervise and/or literature for deeper understanding.
E=k*cos(n*phi - phi0), sort of.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Oct 2022
Posts: 10
J
Forum Member
OP Offline
Forum Member
J
Joined: Oct 2022
Posts: 10
Hi Lennart thank you once more for your kind update:).

Yes the complete line is:

OG311 CG2O2 CG2R51 CG2R51 0.0369 2 180.00 ! 14C+H , from CG2DC1 CG2O5 CG2R51 CG2R51, penalty= 74.5

Henceforth I was unsure of the `from CG2DC1 CG2O5 CG2R51 CG2R51┬┤ portion, I will further research.

Kind Regards,
Joel

Last edited by Joel Subach; 01/31/23 10:04 PM.
Joined: Sep 2003
Posts: 4,881
Likes: 12
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,881
Likes: 12
The comment is just an indication of a similar dihedral from which the parametervalues were taken


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Oct 2022
Posts: 10
J
Forum Member
OP Offline
Forum Member
J
Joined: Oct 2022
Posts: 10
Hello Lennart thank you for your kind update:).

`a similar dihedral from which the parameter values were taken┬┤ was this similar dihedral taken from the same ligand that I had input or from a similar ligand?

Thanks:)

Joined: Sep 2003
Posts: 4,881
Likes: 12
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,881
Likes: 12
Considering the high penalty, and the fact that the atoms are different it is unlikely that your ligand has already been parameterized, Since the penalty is high you should probably do some further validation or optimization. I cannot help you with this.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Page 1 of 2 1 2

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u3 Page Time: 0.017s Queries: 35 (0.013s) Memory: 0.7874 MB (Peak: 0.8864 MB) Data Comp: Off Server Time: 2023-06-05 20:23:21 UTC
Valid HTML 5 and Valid CSS