Re: dimer minimisation and psfgen problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Mar 18 2004 - 17:24:45 CST

On Thu, 18 Mar 2004, Uday Chippada wrote:

> Hi guys,
> I have asked this same question before with no luck.
> How do I apply forces on 3 atoms simultaneously, for eg. if i have 3
> chains, and I want to pull all three chains at same time, how do i
> specify the SMD atom?
The smd atoms are specified in the pdb file that has the occupancy column
set to 1. But I think you know that already.

> I mean to ask is there a way I can figure out which SMD atom is which,
> from thep output log file.
Does the output log show only one line when discribing the position and
velocity and force?

Brian

> Thanx
> Uday.
>
> > "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 **
*****************************************************************

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