VMD-L Mailing List
From: Tahmina Akter (takter_at_aggies.ncat.edu)
Date: Wed Jun 29 2016 - 10:30:56 CDT
Thank you all. I appreciate your comments. Can you please tell me how can I
build my own PMMA pdb?
On Tue, Jun 28, 2016 at 4:10 PM, Pawel Kedzierski <
> 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> wrote:
>> 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
> 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.
>> http://www.wall.org/~larry/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.
>> Tahmina Akter