[gmx-users] Re: about complex MD

[Natapol Pornputtapong]

    I have a protein and I want to check where is the ligand can bind on
my protein. This ligand doesn't come together with the protein. I must
add it after use pdb2gmx.
When I run EM and MD,the ligand is alway in the start coordinate. The
ligand don't move to anywhere and sometime it is kicked out from the
system to stay on the border. If I move the ligand coordinate next to
the protein ,I will interact with the nearest residue and don't move to
the protein pocket. 
    I run EM with steepest descents and PME coulomb type, start PR and
MD with  PME and Berendsen temperature and pressure coupling.

Thank you very much.
Natapol Pornputtapong
Research Assistant Bioinformatics Lab.
National Center for Genetic Engineering and Biotechnology ( BIOTEC)
Thailand
E-mail:natapol.por at biotec.or.th
On Mon, 2005-05-16 at 12:00 +0200, gmx-users-request at gromacs.org wrote:

>    1. about complex MD (Natapol Pornputtapong)
>    2. Re: about complex MD (David)
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 16 May 2005 09:37:22 +0700
> From: Natapol Pornputtapong <natapol.por at biotec.or.th>
> Subject: [gmx-users] about complex MD
> To: Gromacs Users Mailing list <gmx-users at gromacs.org>
> Message-ID: <1116211042.5161.34.camel at localhost.localdomain>
> Content-Type: text/plain
> 
> Now I work on protein-ligand complex by GROMACS. The system that I
> prepare,has a ligand on outer of cell. When I run dynamics the ligand
> cannot soak in to the water and don't react with protein molecule. This
> is the first problem.
> >From past, I change the ligand coordinate to put the ligand into waters
> but when I run dynamics on this system the ligand is kicked from the
> system. What can I do for these problems. Please suggest me.
> 
> Thank you very much
> Natapol Pornputtapong
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 16 May 2005 08:28:41 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] about complex MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1116224921.5059.1.camel at localhost.localdomain>
> Content-Type: text/plain
> 
> On Mon, 2005-05-16 at 09:37 +0700, Natapol Pornputtapong wrote:
> > Now I work on protein-ligand complex by GROMACS. The system that I
> > prepare,has a ligand on outer of cell. When I run dynamics the ligand
> > cannot soak in to the water and don't react with protein molecule. This
> > is the first problem.
> > >From past, I change the ligand coordinate to put the ligand into waters
> > but when I run dynamics on this system the ligand is kicked from the
> > system. What can I do for these problems. Please suggest me.
> 
> Please give more detail. If you have a structure for a complex it will
> most likely stay together. Maybe you just have a PBC effect. Try
> editconf -center and center on the protein.
> 
> > 
> > Thank you very much
> > Natapol Pornputtapong
> > _______________________________________________
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++