AMBER Archive (2006)

Subject: Re: AMBER: leap usage

From: Angelo (
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:

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

You can change it to follow your necessities
Good luck


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
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to