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
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
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 amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 05 2006 - 06:07:30 PST
