[gmx-users] OPLS force field issue....
Sidath Wijesinghe
swijesi at g.clemson.edu
Wed Jan 22 19:13:10 CET 2014
Justin,
i was able to generate the .top file for 3 monomers by making the
corresponding .rtp entry.
below is a segment of my .rtp entry and thr .pdb file i used.
.rtp entry for first few atoms out of 208
[ UNK ]
[ atoms ]
C1 opls_240 0 1
C2 opls_145 -0.12 1
C3 opls_240 0 1
C4 opls_240 0 1
C5 opls_158 -0.12 1
C6 opls_158 -0.12 1
C7 opls_158 -0.12 1
C8 opls_158 -0.12 1
C9 opls_158 -0.12 1
C10 opls_158 -0.12 1
[ bonds ]
C1 C2
C1 C13
C1 C82
C2 C3
C2 H28
C3 C4
C3 C5
C4 C11
C4 C21
C5 C6
C5 H29
and so on....
segment of my .pdb used.
ATOM 1 C1 UNK 1 -0.3884 0.71623 0.01741 1.00 0.00 UNK
ATOM 2 C2 UNK 1 0.52009 1.96858 0.02142 1.00 0.00 UNK
ATOM 3 C3 UNK 1 2.05261 1.8016 0.02832 1.00 0.00 UNK
ATOM 4 C4 UNK 1 2.67378 0.39693 0.04493 1.00 0.00 UNK
ATOM 5 C5 UNK 1 3.00381 3.01293 0.02021 1.00 0.00 UNK
ATOM 6 C6 UNK 1 2.43967 4.44371 0.06547 1.00 0.00 UNK
ATOM 7 C7 UNK 1 3.74954 5.25409 0.04830 1.00 0.00 UNK
ATOM 8 C8 UNK 1 3.66193 6.78984 0.08175 1.00 0.00 UNK
ATOM 9 C9 UNK 1 5.14612 7.20376 0.05800 1.00 0.00 UNK
ATOM 10 C10 UNK 1 5.41193 8.7194 0.08617 1.00 0.00 UNK
ATOM 11 C11 UNK 1 4.20533 0.24061 0.06162 1.00 0.00 UNK
ATOM 12 C12 UNK 1 5.73704 0.08685 0.07550 1.00 0.00 UNK
ATOM 13 C13 UNK 1 0.24354 -0.6927 0.01957 1.00 0.00 UNK
ATOM 14 C14 UNK 1 -0.6215 -1.9681 0.00425 1.00 0.00 UNK
ATOM 15 C15 UNK 1 -2.1484 -1.7855 0.06322 1.00 0.00 UNK
i was able to get the .gro and .top file using pdb2gmx
after that i was using grompp but i got an error message as follows.
ERROR 254 [file topol.top, line 1941]:
No default Ryckaert-Bell. types
ERROR 255 [file topol.top, line 1942]:
No default Ryckaert-Bell. types
ERROR 256 [file topol.top, line 1943]:
No default Ryckaert-Bell. types
i was reading the gmx_users blogs and it specifies that i need to manually
enter the parameters that have errors.
i am not clear with that. could you please tell me what i need to do here.
( when i look the lines regarding the errors they
are pointing out the diheadrals)
Sidath
On Fri, Jan 10, 2014 at 8:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/10/14, 2:20 PM, Sidath Wijesinghe wrote:
>
>> Justin,
>>
>> i was able to obtain the . top file for 3 uncharged monomers. then i
>> used the
>> grompp
>>
>> i got a fatal error as follows....
>>
>> Program grompp, VERSION 4.5.5
>> Source code file: grompp.c, line: 175
>>
>> Fatal error:
>> The largest charge group contains 207 atoms. The maximum is 32.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> what could be the reason for this? do you think i have done some thing
>> wrong?
>>
>
> Yes, the topology is wrong. The error message is fairly explicit. Read
> in the manual about what consists of a good charge group.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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--
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University
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