AMBER Archive (2004)

Subject: Re: AMBER: Leap

From: David A. Case (
Date: Tue Nov 09 2004 - 11:00:38 CST

On Tue, Nov 09, 2004, Greg Kellogg wrote:

> Hi I am currently running Amber 7.0 on Redhat Linux. Is
> there anyway to setup tleap or xleap to run in a batch
> mode? I have 529 structures to convert into prmtop and
> inpcrd and I am looking for an easier way to do it.

Roughly, a C-shell script like this should get you started:

#!/bin/csh -f

foreach i ( *.pdb )

cat <<EOF >
source leaprc.ff03
x = loadpdb $i
saveamberparm x $ $i:r.crd

tleap -f


(Note: this is untested; modify it according to what you really need to do;
if you are unfamiliar with shell programming, you will probably have to do
some reading.)

...hope this helps...dac

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