AMBER Archive (2002)

Subject: Re: topology file generation

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Mon May 06 2002 - 07:11:54 CDT

Hi,
> Hello,
> I would like to automate generation of topology file for a large
> number of PDBs.
...
Provided your pdbs are 'clean', the easiest way to do this
that comes to my mind is using NAB:

the following NAB 'program' reads in a pdb file
and writes out a prmtop file ( named 'prmtop'):

molecule m;
m=getpdb(argv[2]);
leap(m,"","");

so, if you have your pdb files in one directory,
you might do something like (in tcsh and with the above 'program' compiled
to 'makeprmtop' ):

foreach i (*.pdb)
makeprmtop ${i}
mv prmtop ${i}.prmtop
end

hope it helps,
regards
Andreas 

-- 
             
            )))))
            (((((
           ( O O )
-------oOOO--(_)--OOOo-----------------------------------------------------
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
                       svrci_at_tbi.univie.ac.at
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
-------\ (----(   )--------------------------------------------------------
        \_)    ) /
              (_/