[gmx-users] minimized on protein-protein decoys

[Justin A. Lemkul]

Quoting Liu Shiyong <liushiyong at gmail.com>:

> Hi,  Mark,
> Thanks for reply.
>
>
> On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
>
> > 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 ?

Separate your .pdb file into two - each protein in a separate file.  Run pdb2gmx
on each of these .pdb files, and include the output topologies as .itp files in
your system topol.top, i.e.:

protein_A.top --> protein_A.itp
protein_B.top --> protein_B.itp

#include both in your topol.top

Doing this will allow you to see the net charge on each protein.

Using the -missing flag with pdb2gmx is dangerous (as noted in the
documentation).  Is there a reason you're using this option?  If atoms are
missing from your model, that could be a source of some of the net charge
you're seeing.  If your charge is indeed integral, then it is likely due to the
fact that many proteins bear some net charge; most are not perfectly balanced
between positives and negatives!

-Justin

>
> 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
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================