[gmx-users] charge on protein

[David van der Spoel]

On Tue, 2005-01-25 at 22:36 -0800, Gia Maisuradze wrote:
> David,
> 
> Thanks for the answer. I have used genion. Since genion requires to have 
> .tpr input file I have done all steps (generate .top and .gro files, 
> solvate the protein in a periodic box filled with water, 
> energy minimization of protein in solvent) with non-zero charge system. 
> Then I have generated the input for the position restrained mdrun by 
> grompp and got pr.tpr file, which I have used in genion as an input file. 
> I got new pdb file. I have generated new .top and .gro files with zero 
> total charge. I have solvate the protein in water, when I checked new 
> topology file I got two proteins (PROTEIN_A and PROTEIN_B) and two 
> solvents. Then I have done energy minimization, and after that 
> tried to generate input for the position restrained mdrun, but got Fatal 
> error: Not enough ref_t and tau_t values!
> I have used PME in .mdp files.

This has to do with the definition of groups. You may have to add a
group in an index file corresponding to the ions.

> What have I done wrong? How can I fix the problem?
> 
> With best wishes,
> 
> Gia Maisuradze
> 
>   On Tue, 25 Jan 2005, David van 
> der Spoel wrote:
> 
> > 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
> >>>>>> Get Your Private, Free E-mail from Indiatimes at
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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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> >>>>
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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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