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

Justin Lemkul jalemkul at vt.edu
Tue Dec 17 16:26:56 CET 2013

On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe
<swijesi at g.clemson.edu>wrote:

> 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"
I'm suggesting you simplify what you are doing to try to give g_x2top a
break.  It is not very adept at doing what you are trying to make it do.
 You have sodium ions.  They're not bonded to anything.  They don't need to
be considered as one "molecule" along with the rest of the system.
 Therefore, you don't need g_x2top to do anything with them.  In a "normal"
Gromacs workflow, one takes a solute, gets a topology, adds some solvent
(using the #include mechanism for solvent, not generating a whole new
topology), then maybe adds some ions or other small molecules (again
#including a pre-existing topology) and the system is built.  Now
reverse-engineer that.  If you have some small species like ions, why
reinvent the wheel?  You already have their topology in ions.itp, so you
just #include that in your final system topology and write the entry in
[molecules] yourself.

If that's still confusing, please spend some time with tutorials (my own
lysozyme tutorial walks you through topology organization and how Gromacs
normally functions) and the manual, specifically Chapter 5.  Then, once
you're comfortable with the file hierarchy and such, dive into g_x2top with
something simple, like one of your molecules, and make sure you know
exactly what's going on.  Then add more layers of complexity until you get
the result you need or the program breaks completely ;)




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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