AW: Building crystal polymer

From: Norman Geist (
Date: Fri May 17 2013 - 07:39:30 CDT



If your topology building tool is able to add missing atoms, the simplest
way would be to remove all atoms that should not be present with the bond,
and let the tool add everything else. In this case, remove TER from the pdb
between residues that are about to be bonded. I know that one can easily do
it like that with the ambertools, hopefully psfgen is able to also.


Otherwise, writing a tcl script could the job also.


Good luck


Norman Geist.


Von: [] Im Auftrag
von Shaikh Abdul Rajjak
Gesendet: Freitag, 17. Mai 2013 07:59
Betreff: namd-l: Building crystal polymer


Dear NAMD User,

I am new user to NAMD. I would like to build a polymer membrane (ex.
polyethylene difluoride). PVDF membrane is semicrystalline. I have build a
unit cell for PVDF and replicated it 10X10X10 using replicateCrystal.tcl
script. I have created a topology file and parameter file based on PET
tutorial. Please see the attached file for the same. Now I would like to add
bond between each monomer so that it will be polymer and then truncate the
terminal residues. I can define bond manually but system is big. There is
any way to add bond between two monomers. I am unable to generate psf file
using autopsf utility in VMD. I want to do molecular dynamics simulation
using NAMD and then study polymer membrane biomolecular interactions.
Thank you
Abdul Rajjak


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