AMBER Archive (2003)
Subject: Re: question about ligand
From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 31 2003 - 17:14:41 CST
On Fri, Jan 31, 2003, Lishan Yao wrote:
> I try to run MD for a protein complexed with ligand. I prepared prep file
> for ligand. But the problem is when leap reads the pdb file of protein ligand
> complex, it always complains about the atom names of the ligand. I try to
> change these atom names to the names in prep file manually. But I don't know
> whether this is the right way to fix this problem?
It is generally better to change the names in the *pdb* file to match those
in the prep file, but either direction will work. What are the error messages
LEaP writes out? They are usually pretty informative about what doesn't
match between the prep and pdb files.
Send some sample files if you still have problems.
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case