[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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