VMD-L Mailing List

From: Anneta Tzampazi (toulka_at_gmail.com)
Date: Fri Oct 03 2008 - 04:43:19 CDT

I created a graphite substrate using the Inorganic builder plugin. Using the
atomselection command I isolated 150 atoms from this pdb file and saved them
into another pdb file. But whenever I try to create a psf file from the
latter pdb (via psfgen) I can't get the right structure file. It seems that
the psf created only takes into account bonds between atoms of the same
residue, ignoring bonds between atoms of neighbouring residues. Attached you
will find the topology file I used. The wrong psf file must have something
to do with the topology file, but trying to change the IC's, or the bonds,
or the angles gave me no right psf file whatsoever, so any advice is more
than welcome. Thank you in advance.