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

[Justin A. Lemkul]

ram bio wrote:
> 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:
> 

Why would you choose "None?"  It would seem that you do not, in fact, have 
capping groups.  If atom 1 is the N of THR, then there is no ACE cap before it...

> 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)

These messages generally indicate missing atoms.  Investigate what they are and 
why these errors are coming up.

> 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)
> 

This warning comes from the fact that you are telling pdb2gmx to look for 
capping groups in order to find improper dihedrals, and it appears no such 
groups exist.

> 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.
> 

There is a reason the pdb2gmx help information calls the -missing option 
"dangerous"...

> 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.
> 

Find out which atoms are missing (if any) to fix the "long bonds" problem, then 
don't specify "None" as your termini unless you really have acetyl and amide caps.

-Justin

> 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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> 

-- 
========================================

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

========================================