From: Peter Freddolino (
Date: Tue Apr 18 2006 - 09:29:09 CDT

Hi Per,
you normally do need to split things into multiple chains. This can be
done, for example, using the procedures from the gramidicin tutorial
Autopsf, a new VMD plugin available in VMD 1.8.4, can also automate this
task for many systems, so you may want to give it a try.

Per Jr. Greisen wrote:

>I am trying to generate the psf for a dimeric protein consisting of two
>and two ligands. Do you have to strip the pdb file into the different
>parts such as: chainA, chainB, NAD, water etc. or can you do it at once
>load the different topology files - is there an example in any of the
>tutorial to do it ?
>Thanks very