[gmx-users] Generate topology

[Justin Lemkul]

On 7/19/13 10:06 AM, afsaneh maleki wrote:
> Dear Justin
>
> I copied all of files in oplsaa.ff folder in my working directory and
> edited the atomname2type.n2t file as mentioned in before post in my working
> directory.
>
> I used   these command:
>
> ] g_x2top  –f  .pdb  –o  .top  -pbc –ff oplsaa
>
>
>
> And gromacs get me:
>
>
>
> opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t
>
> There are 23 names to type translations in file oplsaa.ff
>
> Generating bonds from distances...
>
> atom 44
>
> Can not find forcefield for atom C21-2 with 3 bonds
>
> Can not find forcefield for atom C18-5 with 3 bonds
>
> Can not find forcefield for atom C16-10 with 3 bonds
>
> Can not find forcefield for atom C20-11 with 3 bonds
>
> Can not find forcefield for atom C15-17 with 3 bonds
>
> Can not find forcefield for atom C12-18 with 3 bonds
>
> Can not find forcefield for atom C7-27 with 3 bonds
>
> Can not find forcefield for atom C5-28 with 3 bonds
>
> Can not find forcefield for atom C3-33 with 3 bonds
>
> Can not find forcefield for atom C2-34 with 3 bonds
>
> Can not find forcefield for atom C9-40 with 3 bonds
>
> Can not find forcefield for atom C10-41 with 3 bonds
>
>
>
> Program g_x2top, VERSION 4.5.4
>
> Source code file: g_x2top.c, line: 206
>
> Fatal error:
>
> Could only find a forcefield type for 32 out of 44 atoms
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
> …………………………………………………..
> I seem can't read atomname2type.n2t file from my working directory.
>

Use "-ff select" to choose the force field that resides in the working 
directory.  Specifying "-ff oplsaa" tells g_x2top to use the oplsaa.ff directory 
in $GMXLIB.

-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

==================================================