[gmx-users] OPLS force field issue....
swijesi at g.clemson.edu
Tue Dec 17 16:49:37 CET 2013
Thank you very much!
On Tue, Dec 17, 2013 at 10:25 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > ATOM 7884 SOD UNK 1 40.1388 -263.52 64.6776 1.00 0.00
> > ATOM 7885 SOD UNK 1 18.3684 -236.89 77.4756 1.00 0.00
> > ATOM 7886 SOD UNK 1 14.5668 -246.09 79.7592 1.00 0.00
> > ATOM 7887 SOD UNK 1 15.7704 -239.23 76.65 1.00 0.00
> > ATOM 7888 SOD UNK 1 14.7888 -242.75 78.6228 1.00 0.00
> > 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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