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

[Justin Lemkul]

On Mon, Dec 16, 2013 at 11:26 PM, sidath1 <swijesi at g.clemson.edu> wrote:

> Justin,
>
> i have added these few lines to the atomname2type.n2t
>
> 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
>
> O  opls_267   -0.495284   15.9994   1 C 0.1214
>
> C  opls_470    0.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214
>
> O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974
>
> H  opls_270    0.417334    1.0079   1 O 0.0974
>
> C  opls_145    0.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387
>
> C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395
>
> H  opls_146    0.110842    1.0079   1 C 0.1087
>
> and then i was able to increase the force field type significantly.
> Fatal error:
> Could only find a forcefield type for 7797 out of 7930 atoms
>
> my pdb file has Sodium ( sodium carboxylate) , what is the best thing that
> i
> can follow afterwards?
>
>
I would just remove the sodium from the configuration given to g_x2top.
 There's no need to reinvent the wheel there.  Sodium parameters are
already in OPLS-AA in ions.itp, so just #include it in the topology for the
other molecule(s) written by g_x2top, like a normal workflow.  Then modify
the [molecules] directive to reflect the sodium ions and proceed with the
intact coordinate file.

-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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