[gmx-users] minimized on protein-protein decoys

Liu Shiyong liushiyong at gmail.com
Sun Mar 9 23:41:03 CET 2008

Hi,  Mark,
Thanks for reply.

On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham <Mark.Abraham at anu.edu.au>

> Liu Shiyong wrote:
> > Hi,  all
> >
> > My purpose is to get the binding energy by gromacs.
> You can't do this without water. The binding energy involves displacing
> water interactions.

     Yes, But I just tried to get the binding energy  by minimizing
protein-protein decoy without water.

> > I tried to minimize protein-protein docking decoy by using gromacs
> > without water. But after being minimized, the ligand ran away from
> > receptor.
> "ran away" during what calculation?

  During minimizing ...
The following is my script.  r-l_1.pdb is a protein-protein decoy structure.

pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing >
output.pdb2gmx 2>&1 &
grompp -f em.mdp -c r-l_1.gro -p r-l_1.top -o input.tpr > output.grompp 2>&1
mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e
minim_ener.edr > output.mdrun 2>&1 &

> > That's not what I expected . I just want to relax the protein-protein
> > interface due to some atom-atom contact crash .
> That's what position-restrained EM or MD is for.

 Yes, I will try position-restrained EM. Thanks for suggestion.

> > By the way, I found the net charge is not zero after adding H atoms on
> > complex by pdb2gmx.  Can I solve the non-zero net charge problem by
> > adding H atom on receptor and ligand
> >
> > separately?
> Depends what's causing the non-zero charge. Integral non-zero charge is
> different from non-integral. Some integral charges are sensible, some
> aren't.

 The method of adding H atom that I used  is
pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing >
output.pdb2gmx 2>&1 &
  It added all H atom on receptor and ligand at the same time.  Is it a
possible reason for Integral non-zero charge ?
 I want to try to add H atom on receptor and ligand , separately.

Do you know how to add H atom on receptor and ligand , separately  , and
combine them into one input file as minimizing ?

If  I was wrong, please point out my mistake. Thanks.

> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080309/b8b31e54/attachment.html>

More information about the gromacs.org_gmx-users mailing list