[gmx-users] Solvating protein

[Sai Pooja]

Now I use genion and it says no ions to add?

Using a coulomb cut-off of 1 nm
No ions to add and no potential to calculate.

command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o
solions.gro -p finalnoss.top


On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja <saipooja at gmail.com> wrote:

> 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.
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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