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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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