From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Oct 02 2006 - 19:57:54 CDT
When you generate your psf, you need to have two segments (and
therefore two pdbs), one for each chain. You can use VMD to first
write out a pdb for each chain. Then you'll need something like this
in your psfgen script:
segment A {pdb A.pdb}
coordpdb A.pdb A
segment B {pdb B.pdb}
coordpdb B.pdb B
Let us know if this isn't clear.
On Oct 2, 2006, at 6:46 PM, Yuqi Liu 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.
>
>
>
>
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