From: P.-L. Chau (
Date: Thu May 17 2012 - 07:42:58 CDT

Thank you for your message.

> VMD does what *you* ask it to do.
> [...]
> VMD is deliberately not trying to be too smart,
> but rather relies on consistent input data.
> so if you want scripts to work well, you have
> to make sure that your selections match the
> indicators that VMD uses. details on that should
> all be listed in the user's guide.

Could I ask you if you could possibly be a bit more specific on what I
should be looking for, please? I have scoured the VMD user's guide, but
have found precious little about splitting files for preparation for NAMD.
Would there be some extra tutorial about splitting files and handling ATOM
and HETATM in pdb files, please?

Thank you very much!

P-L Chau

Bioinformatique Structurale
Institut Pasteur
75724 Paris
tel: +33 1 45688546
fax: +33 1 45688719