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

[Sidath Wijesinghe]

1. could you please tell me what does this mean ? " charge group is
inappropriately large"  the overall charge is appear to zero in my
topology. i am little confused here.

2. if below atoms types in  represent C 1&11...so on  and those atom types
appear in the error....

C    opls_240    0    12.011    3    C 0.142   C 0.142   C 0.142
C    opls_239    0    12.011    2    C 0.142   C 0.142 and if i cannot see
these lines in  ffnonbonded.itp

do i need to add them in ffnonbonded.itp?


On Wed, Jan 22, 2014 at 2:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University