[gmx-users] charge on protein

[David van der Spoel]

On Mon, 2005-01-24 at 19:22 -0800, Gia Maisuradze wrote:
> David,
> 
> Thanks for your reply. I have checked carefully all steps of simulation and 
> found that in the beginning when I generated the topology and structure 
> files by pdb2gmx, one gives that total charge is 1.000e. I used pdb file 
> from protein data bank.  Is that weird or normal?In all steps of 
> calculations I get warning that topology file has non-zero charge. Do I need 
> to add counter-ions in topology file?
> 
use genion.

> Best regards,
> 
> Gia Maisuradze
> 
> 
> ----- Original Message ----- 
> From: "David" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Monday, January 24, 2005 12:55 PM
> Subject: Re: [gmx-users] charge on protein
> 
> 
> > On Mon, 2005-01-24 at 10:59 -0800, Gia Maisuradze wrote:
> >> Hi,
> >>
> >> I also have non-zero charge in my calculations, but it is much less
> >> than -15.000e, it is 1.000e or 2.000e. Is it reasonable to simulate 
> >> protein
> >> with this charges?
> > If you are able to simulate long enough it is best to add counter-ions
> > and use PME.
> >>
> >> Thanks,
> >>
> >> Gia Maisuradze
> >>
> >> ----- Original Message ----- 
> >> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> >> To: "4tejender" <4tejender at indiatimes.com>; "Discussion list for GROMACS
> >> users" <gmx-users at gromacs.org>
> >> Sent: Sunday, January 23, 2005 8:32 AM
> >> Subject: Re: [gmx-users] charge on protein
> >>
> >>
> >> > On Sun, 2005-01-23 at 21:29 +0530, 4tejender wrote:
> >> >> hello users
> >> >>  i m new to gromacs can anyone tell me it is advisable to simulate
> >> >> protein with high charge.does it effect reliablity of the dyanamics. 
> >> >> if
> >> >> yes what is a proper method to reduce the charge. i m getting waring 
> >> >> for
> >> >> a non zero charge of -15.000e during processing protein file.
> >> >
> >> > that is quite a lot. If you don't add ions it may even unfold due to 
> >> > the
> >> > charge. Be careful with a long equilibration of the solvent and ions
> >> > (e.g. run 2-5 ns with position restraints on the protein).
> >> >>
> >> >> thanks in advance
> >> >> teje
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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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> >>
> >> _______________________________________________
> >> gmx-users mailing list
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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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> > 
> 
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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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