Re: dimer minimisation and psfgen problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Mar 17 2004 - 10:18:12 CST

My first guess would be to remove the first writepsf command. One final
writepsf and writepdb will suffice.

regards
Brian

On Wed, 17 Mar 2004, Hua Wong wrote:

> "I maybe wrong but I don't think namd will take more than one psf file."
>
> No, you are not wrong :). Namd will even blurt out an error message specifying that you try to load two structure files.
>
> "In any case you can (and should) combine this file using psfgen. Just
> make sure to assign the chains different segment IDs and things will be
> fine..."
>
> That's what I want to have help about. I want to run a minimisation on a dimer but I am unsure about how to achieve this...
>
> here is the script I use with psfgen
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> topology top_all22_prot.inp
>
> segment IL8A {
> first NONE
> last NONE
> pdb IL8A.pdb
> }
>
> patch DISU IL8A:7 IL8A:34
> patch DISU IL8A:9 IL8A:50
>
> coordpdb IL8A.pdb IL8A
>
> writepsf output/IL8A.psf
>
> segment IL8B {
> first NONE
> last NONE
> pdb IL8B.pdb
> }
>
> patch DISU IL8B:7 IL8B:34
> patch DISU IL8B:9 IL8B:50
>
> coordpdb IL8B.pdb IL8B
>
> writepsf output/IL8B.psf
>
> guesscoord
> writepdb output/IL8dimr_out.pdb
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> What do I have to write in order to obtain a single psf with the two segment?
>
> Thanks.
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:07 CST