[gmx-users] OPLS force field issue....

[Justin Lemkul]

On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote:
>   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
>

I can almost guarantee that charge group is inappropriately large.  Charge 
groups generally have no more than 3-4 atoms (see the manual).

>   [ 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)
>

You need to check those lines for what the atom types are for those atoms. 
Parameters are not present in ffbonded.itp for that sequence of atoms so you 
need to add suitable parameters.

-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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