How can I do protein complex's simulation?

From: Yuqi Liu (
Date: Mon Oct 02 2006 - 18:46:13 CDT



I am a newbie here. I'm trying to build a model of my protein-peptide
complex and do simulation of the complex in NAMD.


I can use the homology modeling to get the initial pdf file which contains
both of the chains. But I can not use psfgen script to generate the
corresponding psf/pdb file of the complex properly ----- the two chains
seemed linked together and became one. Definitely I can generate psf files
for the two chains separately. Then I have no idea how to merge the two psf
files to one to start the simulation.


My questions are


How to generate the psf file for the complex and is there a standard scheme
for protein complex's simulation?



Thanks a lot.


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