AMBER Archive (2002)

Subject: Re: a leap question

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Oct 17 2002 - 08:43:24 CDT

Hi, Vlad,
    I have this script that can do this provided your pdb files don't
    need special care :)

#!/bin/tcsh

foreach PDB (`ls *.pdb`)
    cat > leap.in << EOF
    m = lp $PDB
    saveamberparm m $PDB:r.top $PDB:r.crd
    quit
EOF
    tleap -f leap.in
    rm -f leap.in
end

    You can add any leap commands as you need.

    Regards,

On Thu, 17 Oct 2002, Vlad Cojocaru wrote:

> Dear Amber users,
> First of all I am sorry if my questions sometimes are trivial and
> maybe I can find the answers easy looking in the archive. I hope I did
> not bother anybody. I think the list is less time consuming for finding
> these answers. Please if you do not find time for short answers just
> throw the emails to trash.
>
> Ok I have a question about leap:
> Is there a way in leap to load at once a bunch of pdbs and to save the
> topology and coordinate files? Something like foreach loop? If somebody
> knows how to do that could you please give me some hints. I tried with a
> shell script
> but I couldn't pass variables from the shell to leap.
>
> All the replies are highly appreciated,
> Best wishes,
> vlad
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790