[gmx-users] charge on protein

[Gia Maisuradze]

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.
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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>>>>> --
>>>>> 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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