VMD-L Mailing List

From: Gkourmpis, Thomas (Thomas.Gkourmpis_at_borealisgroup.com)
Date: Tue May 22 2012 - 08:21:12 CDT

Hello everyone

Can anyone help me a bit on how to build a polymer using VMD/Molefacture/psfgen?

I read this thread http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8383.html but somehow I got even more confused.

Here is what I do.

I have a butane pdb file (made using Avogadro) and I load it to molefacture where I do add hydrogens. Since this is my basic monomer (let's say I want to build Polyethylene to make it simple) I do not add three hydrogen atoms to the first and last carbons (C1 and C4) as to allow for the chain connectivity.

After that I build the pbd file using molefacture and this is what I get

       3 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS topology /work5/stgkouth/test/molecule.top
 REMARKS segment MOL { first NONE; last NONE; auto angles dihedrals }

      12 !NATOM
       1 MOL 1 LIG C1 C3 0.000000 12.0107 0
       2 MOL 1 LIG C2 C3 0.000000 12.0107 0
       3 MOL 1 LIG C3 C3 0.000000 12.0107 0
       4 MOL 1 LIG C4 C3 0.000000 12.0107 0
       5 MOL 1 LIG H H 0.000000 1.0079 0
       6 MOL 1 LIG H2 H 0.000000 1.0079 0
       7 MOL 1 LIG H3 H 0.000000 1.0079 0
       8 MOL 1 LIG H4 H 0.000000 1.0079 0
       9 MOL 1 LIG H5 H 0.000000 1.0079 0
      10 MOL 1 LIG H6 H 0.000000 1.0079 0
      11 MOL 1 LIG H7 H 0.000000 1.0079 0
      12 MOL 1 LIG H8 H 0.000000 1.0079 0

      11 !NBOND: bonds
       1 2 1 9 1 10 2 3
       2 5 2 6 3 4 3 7
       3 8 4 11 4 12

      18 !NTHETA: angles
       1 2 6 1 2 5 1 2 3
       2 3 8 2 3 7 2 3 4
       2 1 10 2 1 9 3 4 12
       3 4 11 3 2 6 3 2 5
       4 3 8 4 3 7 5 2 6
       7 3 8 9 1 10 11 4 12

      21 !NPHI: dihedrals
       1 2 3 4 1 2 3 7
       1 2 3 8 2 3 4 11
       2 3 4 12 3 2 1 9
       3 2 1 10 4 3 2 5
       4 3 2 6 5 2 1 9
       5 2 1 10 5 2 3 7
       5 2 3 8 6 2 1 9
       6 2 1 10 6 2 3 7
       6 2 3 8 7 3 4 11
       7 3 4 12 8 3 4 11
       8 3 4 12

       0 !NIMPHI: impropers

       0 !NDON: donors

       0 !NACC: acceptors

       0 !NNB

       0 0 0 0 0 0 0 0
       0 0 0 0

       1 0 !NGRP
       0 0 0

I know I am missing an initial and final monomer units, but these can be made (I guess so please correct me if I am wrong) in the same way by adding an extra hydrogen to C1 and C4 respectively thus making two new files.

When I try to use psfgen I seem unable to load more than this single pbd file and I cannot create the polymer chain.

I am sure I do something silly here but I just cannot understand what that is. Any help would be most appreciated

Thanks a lot in advance

Thomas Gkourmpis

Thomas Gkourmpis
Researcher
Borealis AB | SE-444 86 Stenungsund | Sweden
Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49
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