VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Jun 28 2016 - 15:10:23 CDT

W dniu 28.06.2016 o 20:50, Ashar Malik pisze:
>
> It is hard to make sense of the pdb you are using. What does it
> contain or supposed to contain? To make a PSF file you need to have a
> well formed pdb such that the atom types and residue names are defined
> in the topology file or vice versa.
>
> On Jun 29, 2016 06:32, "Tahmina Akter" <takter_at_aggies.ncat.edu
> <mailto:takter_at_aggies.ncat.edu>> wrote:
>
> Hello,
> I am very new in VMD. I downloaded a PMMA pdb file from
>
Apart from what Ashar Malik wrote above: you use the standard CHARMM
topology file which provide bonding, atom types and charges for
biomolecular systems but not for arbitrary molecules. So not only the
PDB file should be rewritten (to provide division into monomers, and
unique atom names within monomers) but you also need a topology file for
your system.
There is a "Topology File tutorial" on
www.ks.uiuc.edu/Training/Tutorials/ which you may find useful to
understand the concepts and to create the topology file yourself in case
you don't find something ready for PMMA.
Pawel

> http://www.wall.org/~larry/onion3/pdb/
> <http://www.wall.org/%7Elarry/onion3/pdb/> .
> Now I want to generate the psf file. I tried the AutoPSF. But it
> says Error: failed on end of segment Molecule Destroyed By Fatal
> Error. I am attaching what I did.
>
> Thanks
>
> Regards,
>
> Tahmina Akter
>