From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 01 2014 - 09:30:24 CDT

Hi Ramin,

Split your pdb into two pieces, since a protein segment is meant to
convey that everything in that segment is connected. You can make two
pdb files (chainA.pdb, chainB.pdb), and then do the following:

package require psfgen
topology top_all36_prot.rtf
topology top_all36_cgenff.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {pdb chainA.pdb}
coordpdb chainA.pdb A
segment B {pdb chainB.pdb}
coordpdb chainB.pdb B
guesscoord
writepdb test.pdb
writepsf test.psf

This will get you further along. When generating structures, you should
check to make sure you added in any disulfide bonds that are present,
the termini patches are what you expect them to be, and it is also
usually prudent to check protonation states as well that are known to be
important.

Cheers,
-Josh Vermaas

On 04/01/2014 08:24 AM, Ramin Ekhteiari wrote:
> Hi,
>
> I would like to generate psf file for a dimer protein (i.e., chain A
> and B).
> I tried this tcl commands ,
>
> package require psfgen
> topology top_all36_prot.rtf
> topology top_all36_cgenff.rtf
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> segment U {pdb protein.pdb}
> coordpdb protein.pdb U
> guesscoord
> writepdb test.pdb
> writepsf test.psf
>
> But the it generates only for one chain not more.
> Would you please advise me on how to do it for both chains.
> Would be grateful for any help.
>
> Cheers,
> Ramin.