Re: How do we combine chains in the end

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Feb 02 2004 - 11:54:51 CST

Hi,

You only split the different chains in the PDB file so that you can load
them into psfgen as separate segments. You then create a single psf/pdb
file containing all three chains, as well as solvent, lipid, etc., and
minimize/equilibrate the system as a whole.

-Jim

On Sat, 31 Jan 2004, Uday Chippada wrote:

> Hi all,
>
> When we do minimization and equilibration for protein complexes with
> chains A, B and C etc. we use
>
> set chainA [atomselect top "chain A"]
> $chainA writepdb chainA.pdb
> etc ..
>
> to divide the original pdb file into seperate chains and then do the
> equilibration. Now, my question is how do we combine these together, in
> the end, to know the displacement of an atom when a force is applied,
> with all three chains together?
>
> Any help is appreciated.
>
> Thank you.
> Uday Chippada.
>
>

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