VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 12 2010 - 11:32:10 CST

On Fri, 2010-03-12 at 10:41 -0600, muniyamuthu.raviprasad_at_ndsu.edu
wrote:
> Hi All
>
> I am working on polymers. I need to connect individual monomers to make
> polymers. I can connect two monomers using patch but if I want to connect
> three or more monomers I need to create patches for each and every
> connection point. Is there any other way to connect ? That might helpful
> to make very long polymers without doin too many patches.

ravi,

for this kind of system, you may be better off not using psfgen
at all. if you have a regular bonding pattern and have already
coordinates generated, then you may be able to use the "guess"
methods in the topotools plugin to do the job. the scenario that
you describe, is pretty much what i had in mind, when writing
those.

the workflow would be roughly the following.
- generate coordinate file (in xyz or pdb format)
- load into VMD
- generate a selection for each atom "name" and
  then assign the corresponding force field "type"
  in your parameter file
- package require topotools 1.1
  topo guessangles
  topo guessdihedrals
  topo guessimpropers # only if you have double bonds in your polymer
- assign additional information (mass, charge, residue number,
  residue name, chain id) as needed
- write out a psf file: animate write psf new.psf
  write out a pdb file: animate write pdb new.pdb
- double check if everything is ok. with topo getXXXXlist commands
- if you need to augment bonds manually, you can use
  topo addbond <id> <id> or topo delbond

this may be a bit more elaborate at first and would be inefficient
to build protein topologies, but for polymers it would be much
easier, since there is little variety.

to have access to the "guess" functions you have to download
either the latest VMD alpha test version or update your topotools
package to version 1.1 from here:
http://sites.google.com/site/akohlmey/software/topotools

cheers,
   axel.

>
>
> Thanks
> Ravi
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.