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

[Justin Lemkul]

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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