Amber Users
I'm attempting to run a mmpbsa/gbsa calculation on a ligand, receptor system. I have all the required parmtops - solvated complex, complex, receptor and ligand and a 10 nsec MD run. Before running the scripts my system is intact and visualization shows no issues. Once the co-ordinates are extracted, the receptor is fine, and the ligand is mostly intact. However, a sugar ring in the ligand is completely mangled. This occurs with both Python and Perl scripts. I am using Amber 10.0 - does anyone have any suggestions?
I have already checked the naming conventions, and tried reproducing the parmtop files. Why does it only affect 1 sugar ring, when the rest of the ligand is ok?
Thanks in advance
Nicholas Rakowski
Email: nickkowski.yahoo.co.uk
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 21 2012 - 06:00:02 PST
