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

[Sidath Wijesinghe]

Justin,

so that means delete these lines "
 ATOM   7882 SOD  UNK     1       42.69 -261.86  64.056  1.00  0.00      UNK
ATOM   7883 SOD  UNK     1       39.09 -260.89 62.8968  1.00  0.00      UNK
ATOM   7884 SOD  UNK     1     40.1388 -263.52 64.6776  1.00  0.00      UNK
ATOM   7885 SOD  UNK     1     18.3684 -236.89 77.4756  1.00  0.00      UNK
ATOM   7886 SOD  UNK     1     14.5668 -246.09 79.7592  1.00  0.00      UNK
ATOM   7887 SOD  UNK     1     15.7704 -239.23   76.65  1.00  0.00      UNK
ATOM   7888 SOD  UNK     1     14.7888 -242.75 78.6228  1.00  0.00      UNK

i have total of 48 sodium atoms...
 correspond to all the sodium atoms in test.pdb file and let it run with
g_X2top?

i am not clear about what u meant here...

"Then modify
the [molecules] directive to reflect the sodium ions and proceed with the
intact coordinate file"

Thank you!

Sidath




On Tue, Dec 17, 2013 at 8:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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