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

[Sidath Wijesinghe]

Justin,

Thank you for the reply. so that means i need to place the parameters in
atomname2type.n2t file?

i am little confused here....

Thank you!

Sidath



On Mon, Dec 16, 2013 at 4:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Mon, Dec 16, 2013 at 4:06 PM, Sidath Wijesinghe <swijesi at g.clemson.edu
> >wrote:
>
> > Dear Friends,
> >
> > i have done a MD simulation using OPLS/AA in lammps which contains 7930
> > atoms.
> > i want to run this in Gromacs
> >
> > so i followed this step
> >
> >  g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc ( test.pdb is
> the
> > pdb i obtained from my simulation)
> >  after that it was trying to find the parameters from
> > oplsaa.ff/atomname2type.n2t
> > There are 23 name to type translations in file oplsaa.ff
> > Generating bonds from distances...
> >
> > and i got an error as following
> >
> > Fatal error:
> > Could only find a forcefield type for 7100 out of 7930 atoms
> > For more information and tips for troubleshooting, please check the
> GROMACS
> >
> > i have no idea what and where i need to work on to solve this problem.
> > please be kind enough to help me out with this
> >
> >
> g_x2top is not magic, and it is only as smart as the information you
> provide it.  The output indicates that 830 atoms are not described by the
> available entries in the .n2t file.  Refer to
> http://www.gromacs.org/Documentation/File_Formats/.n2t_File for
> information.  The screen output should indicate which atoms are
> problematic.  You will have to amend the existing file, which by default
> only covers the most trivial of molecules.
>
> -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