AMBER Archive (2006)

Subject: Re: AMBER: leap usage

From: Angelo (angelo_at_holmes.cancres.nottingham.ac.uk)
Date: Thu Nov 02 2006 - 10:39:57 CST

Caro Stefano (Dear Stefano),

U can create a loop to create top and crd files for your different pdb
files, something like this:

#!/bin/csh
# Creating topology and coordinate files for each AMBER pdb
foreach in ( `ls -1f yourfile.{?,??,???,????}.pdb`)
set name=${in:r}
echo "source leaprc.ff03" > leap.in
echo "x = loadpdb $name " >> leap.in
echo "saveamberparm x $name.top $name.crd" >> leap.in
echo "quit" >> leap.in
tleap -f leap.in > leap.log
end

You can change it to follow your necessities
Good luck

Angelo

Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:

>Dear Amber Users,
>
> We would like to create a series of .top files from pdb files having one
>mutation each. Is it possible to use leap in a non interactive way, so that it
>is possible to create the files automatically (with some scripting) without
>opening manually every single pdb file?
>
> Thank you in advance
>
> Stefano Pieraccini
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