[gmx-users] Re: about complex MD

[David van der Spoel]

On Tue, 2005-05-17 at 10:06 +0700, Natapol Pornputtapong wrote:
>     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.
Don't you want to run a docking program instead? Try autodock.
> 
> 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
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > -- 
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
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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
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