[gmx-users] charge on protein

[Gia Maisuradze]

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?

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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> -- 
> 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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