Hi Amber users,
I am attempting to do mmgbsa binding energy calculations on a multi-subunit
protein system. I am using ante-mmpbsa.py for creating the complex,
receptor and ligand topology files. The system has 1629 amino acid residues
with 1 ligand.
When I specify the ligand resid ID I get the following error...
Creating ligand topology file by stripping !(:2495) from complex.prmtop
Error: Creating ligand topology failed!
Loaded Amber topology file complex.prmtop
Reading input from STDIN...
> Removing mask '!(:2495)' (69614 atoms) from the topology file.
IndexError: list index out of range
When I specify the ligand Resname It seems to work fine, but the ligand is
not stripped from the receptor file for some reason.
Any Idea what the problem could be? Is ante-mmpbsa.py built to handle big
proteins?
--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Tue Mar 19 2013 - 10:30:03 PDT
