Dear Sir
I am currently using Antechamber for preparing files to run MD on a docked complex. It works fine and I get the prepi and frcmod files. The problem is that the conformation of the ligand within the protein is being changed. What could be the problem? Also I understand that Antechamber runs using AM1, what would be the command for using PM3 instead? The commands I am currently using for the preparation of files are:
nohup $AMBERHOME/exe/antechamber -i LIG.pdb -fi pdb -o LIG.prepin -fo prepi -c bcc -s 2 &
$AMBERHOME/exe/parmchk -i LIG.prepin -f prepi -o LIG.frcmod
The ligand is not charged and I am using AMBER 12 on a GTFORCE TITAN card.
Regards
Mahmood Jasim
PhD Student
Aston University
Birmingham
UK
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Received on Fri Sep 13 2013 - 06:30:04 PDT
