[gmx-users] neutralizing membrane protein in lipid bilayer +water

[ram bio]

Dear Gromacs Users,

Thanks Justin and Marc for the response and you were right.

As suggested, i had a view in the modelled protein pdb file and here
both the terimus are capped that is as follows;

ATOM      1  N   THR A  62     -43.095   3.360  19.026  1.00 30.00           N1+

ATOM   4804  OXT PRO A 355     -53.907  34.064  13.899  1.00110.00           O1-

then i tried to execute the pdb2gmx command as under, (which i did
earlier also): pdb2gmx -f damgomu.pdb -o damgomu_processed.gro -ignh
-ter -water spc

and selected the "Gromos96 53a6" parameter and "none" options, then
the warnings and errors where as follows:

Now there are 294 residues with 3043 atoms
Making bonds...
Warning: Long Bond (12-14 = 0.65447 nm)
Warning: Long Bond (1975-1977 = 4.21722 nm)
Warning: Long Bond (2050-2052 = 3.24295 nm)
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat

WARNING: atom H is missing in residue THR 1 in the pdb file
         You might need to add atom H to the hydrogen database of residue THR
         in the file ff???.hdb (see the manual)

Fatal error:
There were 1 missing atoms in molecule Protein_A, if you want to use
this incomplete topology anyhow, use the option -missing

and in the previous run i concatenated -missing option and continued
further, then the toplogy was written with the charge of Total charge
12.690 e ,but still the warning persisted of missing H atom in THR1.

Please suggest me how to rectify this error and why the total number
of atoms in pdb file (4815) are not matching even though the number of
residues are matching after pdb2gmx step.

Thanks,

Ram





and selected choose the "Gromos96 53a6" parameter and "none" options




On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Gromacs users,
>>
>> I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the system and i learnt from Justin tutorial that we can even neutralize it using -conc and -neutral options in conjugation. As I am running a membrane-protein simulation, I would like to know the command which I am using is correct or not.
>>
>> genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 12 -neutral
>>
>> If my command is wrong Please suggest the right one as In future i have to conjugate SOL and CL- ions to create a special index file.
>>
>>
>
> If your protein has a net charge of +12.69, it is probably wrong.  Does anything in real life have such a net fractional charge?
>
> Go back and evaluate what you have done.  Are there missing atoms?  Wrong parameters?  The genion command you want to use is fine, but is not suitable for your system in its current state.
>
> -Justin
>
>> Thanks
>>
>> Ram
>>
>>
>> ------------------------------------------------------------------------
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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