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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 18:19:09 CEST 2009 

ram bio wrote:
> Dear Justin,
> 
> When I observed the toplogy file the first THR moeity was missing in 1
> hydrogen atom compared to other Thr in the file so i added one line
> below the 1st atom nitrogen for hydrogen as under and corrected the
> qtot to 0,
> 
> 1          N      1    THR      N      1      -0.31    14.0067   ; qtot -0.31
> 2          H      1    THR      H      1       0.31      1.008   ; qtot  0,
> 
> keeping the rest  as the same, and executed the command pdb2gmx and
> selected the same force field and 1 and 1 for n-terminus and
> c-terminus, and now there were no errors as under:
> 
> Now there are 294 residues with 3047 atoms
> Making bonds...
> Warning: Long Bond (14-16 = 0.65447 nm)
> Warning: Long Bond (1977-1979 = 4.21722 nm)
> Warning: Long Bond (2052-2054 = 3.24295 nm)
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Number of bonds was 3113, now 3108
> Generating angles, dihedrals and pairs...
> Before cleaning: 4938 pairs
> Before cleaning: 6118 dihedrals
> There are 1565 dihedrals, 1646 impropers, 4562 angles
>           4938 pairs,     3108 bonds and     0 virtual sites
> Total mass 33592.608 a.m.u.
> Total charge 13.000 e
> Writing topology
> 
>  but, when i saw the topology file , the same number of atoms are
> present and no change in the qtot...
> 
> Why is it that qtot of 13 and the increased number of atoms are not
> shown in the toplogy file and whether have i selected the wrong
> options or is it the wrong way of correcting the toplogy file...
> 

You can't correct a topology and expect it to have any influence on pdb2gmx.
The *output* of pdb2gmx is a topology, so any ad hoc changes after the fact will
mean nothing to another execution of pdb2gmx.  It is generally a very BAD idea
to make such changes - consider that if you add an atom, every single atom
number after will be wrong with respect to bonds, angles, dihedrals, etc.

Your broken topology was a result of the fact that you specified capping groups,
therefore the termini were non-titratable and were not assigned any sort of
reasonable protonation state.

-Justin

> 
> Thanks,
> 
> Ram
> 
> On Tue, Sep 29, 2009 at 8:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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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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