AMBER Archive (2004)

Subject: RE: AMBER: antechamber

From: Ross Walker (
Date: Thu Jul 15 2004 - 13:21:44 CDT

Dear Xin,

> >antechamber -i Ligand.pdb -fi pdb -o Ligand.prep -fo prepi -c bcc
> >parmchk -i Ligand.prep -f prepi -o Ligand.parm
> In xleap:
> >source leaprc.ff99
> >source leaprc.gaff
> >loadamberprep Ligand.prep
> >loadamberparams Ligand.parm
> and then load the protein/ligand complex, save the paramter
> files for MD
> >M=loadpdb protein.ligand.pdb
> >saveamberparm M M.crd
> Is there a better way to do that?
> Thank you for your suggestion.

Not really. Ideally such a thing should be too automated as that makes
mistakes much harder to spot. However, if you wanted to automate this you
could always use tleap and have it source a command file. If you load xleap
and go through the stages you want exactly you will get a leap.log file.
This you can then source using tleap with tleap -s leap.log and it will
carry out the same commands you did. In this way you can put all of the
commands into a single shell script that you can run from the command line.
Thus if you had say a 100 different ligands to create prmtop files for you
could write a script that creates a file containing the leap commands you
want, run antechamber and then tleap and then writes the commands for the
next ligand etc etc.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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