[gmx-users] Solvating protein

[Sai Pooja]

I checked topology file but going with grompp makes sense. Thank you.

On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Pooja wrote:
>
>> Well thats the thing. I have checked my pdb files. All residues have
>>
>
> There aren't charges in a .pdb file, unless you've somehow added them into
> one of the fields yourself.  The file you need to check is your topology.  A
> running value of the net charges is given in the [atoms] directive.  Charges
> are assigned by pdb2gmx based on what is expected in the .rtp file and what
> you chose to assign in terms of protonation state.
>
>
>  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
>>
>
> genbox reads coordinate files, so I don't know how any charge it prints is
> meaningful.  It tells me there is a zero charge on a lysozyme system that I
> know has a +8 charge (regardless of whether or not I pass it a topology as
> well), so don't believe genbox.  Believe grompp.  The magnitude is indeed
> due to small rounding errors.  It should be interpreted as -1.
>
> -Justin
>
>  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<mailto:
>> 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.
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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