Re: How can I do protein complex's simulation?

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Mon Oct 02 2006 - 19:58:29 CDT

Hi liu
        you have to make two different pdb file for your chains. then you
have to create psf and pdb file with these chains as two different segment.
here is the script that i have used to model my protein with two chain.

package require psfgen

topology top_all27_prot_lipid.inp

pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD

segment A {pdb chain_A.pdb}
coordpdb chain_A.pdb A

segment B {pdb chain_B.pdb}
coordpdb chain_B.pdb B

guesscoord

writepdb prodh1.pdb
writepsf prodh1.psf

exit

hope it will help.

On 10/2/06, Yuqi Liu <liuyuqi_at_hotmail.com> wrote:
>
> Hi NAMD,
>
>
>
> 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.
>
>
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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