VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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
(http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/).
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.
Best,
Peter

Per Jr. Greisen wrote:

>Hi,
>
>I am trying to generate the psf for a dimeric protein consisting of two
>chains
>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
>
>
>
>