[gmx-users] Solvating protein

[Sai Pooja]

Well thats the thing. I have checked my pdb files. All residues have either
0 or integer net charges. The number 0.9999994 seems like a rounding off
error especially since the output of genbox says that the system has zero
net charge. Again, I encounter this no-zero net charge when I run grompp
with an mdp file for energy minimization with the protein( excluding
hydrogen ) restrained.

I am using the charmm implemented version of gromacs.

Pooja

On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 10/07/2010 1:28 AM, Sai Pooja wrote:
>
>>
>> Hi,
>>
>> When I start from a energy minimized protein in vacuum and solvate it
>> using genbox, the output message says that the protein has zero charge. So I
>> skip the genion step. I follow this with energy minimization of the solvated
>> protein followed by restraining the protein and then doing a short mdrun (as
>> is the usual procedure outlined in most tutorials). However, when I run the
>> grompp command as the first step for the position restrained md, it runs but
>> prints a note saying that the system has non-zero charge ~ -  0.9999.
>>
>> NOTE 2 [file finalnoss.top, line 8070]:
>>  System has non-zero total charge: -9.999994e-01
>>
>> I dont understand. Do I need to run the genion step anyway or is it okay
>> to continue with this system?
>>
>
> I'd believe grompp before genbox. Surely you know already what is in your
> system, and thus its total charge. You should already know the protonation
> state of all of your relevant protein residues, because you made choices for
> them with pdb2gmx.
>
> Mark
>
>
>
>> Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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