Re: a leap question

From: CUI, Guanglei <>
Date: Thu 17 Oct 2002 09:43:24 -0400 (EDT)

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


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

    You can add any leap commands as you need.


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
Received on Thu Oct 17 2002 - 06:43:24 PDT
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