From: Axel Kohlmeyer (
Date: Mon Jan 14 2008 - 03:39:58 CST

On 1/14/08, Sridhar Acharya <> wrote:
> I would like to know if there is script method to load several pdb molecules
> in batch mode and save them in mol2 format without using GUI.

yes. something like the following:

foreach p {file1.pdb file2.pdb file3.pdb} {
  set m [mol new $p]
  animate write mol2 "$p.mol2" $m
  mol delete $m

for details please have a look at the description of the mol and animate
commands and consult your favorate tcl tutorial.



Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.