AMBER Archive (2003)

Subject: question about ligand

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Fri Jan 31 2003 - 16:43:39 CST

Hi:
   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?

Lishan Yao
Chemistry department
MSU, East Lansing
MI, 48823