On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote:
HI,
I want to simulate helical peptide in TFE-water (1:1 vol) solvent.
1. From previous searches, I got to know that tfe.itp is present in
gmx.ff folder. Can I use this itp file by including it in my top file
generated during pdb2gmx.
Since that file requires the use of the deprecated (i.e. don't use it) gmx.ff
force field, I wouldn't.
2. I also got TFE-water (1:1 vol) pdb and gro pre-equilibrated system
from ATB site. I dont know if I can use either this pdb or gro file
during genbox step for -cs flag
Sure, if it suits your purpose. See also
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents.
-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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