From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Oct 28 2004 - 18:08:26 CDT
Hi
The column that fixed atoms can be specified, but the easiest thing to do
is just change the value by hand in VI based on the segid.
Your statement is a little confusing, what do you want to hold fixed
during dynamics? The protein or the surroundings?
Regards
Brian
On Thu, 28 Oct 2004, Charles Danko wrote:
> Hi,
>
> Question: I am trying to do a dynamics run with a fixed protein but
> allowing the water and lipid to equilibrate around the structure. How
> do I build the pdb file which fixes all atoms except the protein?
>
> I have tried a suggestion found on a webpage in a slightly different
> context, but the result is that all atoms in the system are fixed.
> The details of what I have already tried is listed below:
>
> To fix the system, I am using very simple commands:
> fixedAtoms on
> fixedAtomsFile CONS.pdb
>
> I used VMD to build CONS.pdb, with the following commands at the
> suggestion of a webpage I found.
> > mol load psf SYSTEM.psf pdb SYSTEM.pdb
> > atomselect top all
> atomselect0
> > atomselect0 set beta 0
> > atomselect top {protein}
> atomselect1
> > atomselect1 set beta 1
> > atomselect0 writepdb CONS.pdb
>
> If I load the pdb file, I can set color-mode to beta, and the protein
> is blue while the rest of the system is red.
>
> Under the structure summary, I am receiving the message
> Info: 66547 atoms
> …
> Info: 66547 fixed atoms
>
> Thanks for the help,
> Charles
>
*****************************************************************
**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 - 15:38:57 CST