[AMBER] Antechamber

From: Jasim, Mahmood (Student) <"Jasim,>
Date: Fri, 13 Sep 2013 13:15:48 +0000

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.

Mahmood Jasim
PhD Student
Aston University
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Received on Fri Sep 13 2013 - 06:30:04 PDT
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