On 9/28/13 11:20 AM, bipin singh wrote:
Hi all,
I want to put off constraint between some bonds in my system based on their
atom numbers but the .gro file and .top file atom numbers do not match,
because I used .pdb file to generate this .top file using pdb2gmx. (the top
files contains the atom numbers based on this initial input .pdb file and
the subsequent .gro file contains different atom numbering)
I know that grompp generate constraints based on atomtypes in .top file but
If I use the .pdb file (used during pdb2gmx) to do this will it be fine,
as I will be using this .top file with .gro file for grompp.
As with all bonded interactions, the numbers in the coordinate file are
irrelevant. You can only specify bonded interactions based on the atom numbers
in the [moleculetype] in the .top file.
-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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