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

[Sidath Wijesinghe]

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
>  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
>
> --
>
> ==========================================
>
> 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
>
>
> ==========================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



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