[gmx-users] The structure property

[Tsjerk Wassenaar]

Hi Lin,

Justin is right on all points. The first is indeed a check you should
always perform, but in this case (1LW9), there are no missing
residues/atoms. The point is that one should be aware that there
could. The same thing goes with the hint for the histidines. I could
have not written you should check for missing residues/atoms and mind
protonation states, but then you might take it for granted in any
structure, thus running into problems or just making the MD program an
expensive random number generator.

Anyway, I'll probably polish the tutorial somewhat in the near future
(and expand the analysis part). Do note that this mailing list is not
the mailing list for the tutorial ;) Comments and questions primarily
relating to the tutorial rather than to Gromacs are better sent to me
personally.

Cheers,

Tsjerk


On Fri, Oct 24, 2008 at 9:23 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Chih-Ying Lin wrote:
>>
>> Hi
>>  From the following tutorial, the protein pdb file is downloaded from the
>> Protein Data Bank. Before running the MD simulation, we have to make sure
>> the structure property. I have some questions about this tutorials.
>>
>> http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
>>
>> 1. Make sure that there are NO Missing residues, missing atoms-
>>   http://www.rcsb.org/pdb/files/1lw9.pdb
>>    "Search for the presence of REMARK entries with numbers 465 and/or 470.
>> " => there are no REMARK 465 and REMARK 470  ???
>>
>>
>
> These REMARK lines would correspond to missing atoms or residues.  You
> should always search a .pdb file for such lines; I believe that is the point
> being made.
>
>> 2. The protonation state and side chain orientation of histidine residues
>> may be problematic. => How could I know if they are problematic? => How to
>> do the protonation process on the system?
>>
>>
>
> It is dependent on the protein, and histidines should be protonated
> according to hydrogen bonding networks, whether or not they are involved in
> catalysis (and how the protonation state might affect the active site!),
> coordination of metal ions, etc.
>
> Gromacs will try to guess the appropriate protonation state.  It is your job
> to thoroughly research your system and determine if any special
> considerations are necessary.
>
>> 3. From the tutorial => "Note the numbers of ions added, and verify that
>> an excess of 8 chloride ions is added for neutralization. Having replaced a
>> number of water molecules with ions, the system topology in 1LW9.top is not
>> correct anymore. Edit the topology file and decrease the number of solvent
>> molecules. Also add a line specifying the number of NA+ ions and a line
>> specifying the amount of CL-. "  => Would you please explain this more?
>
> What genion does is replace water molecules with ions.  So if 8 Cl- are
> added, then 8 water molecules are removed.  The corrections to the topology
> are thus trivial to implement.  Otherwise, you can pass the -p flag to
> genion and have it make the changes for you.
>
> -Justin
>
>>
>> Thank you very much
>>
>> Lin
>>
>>
>>
>>
>>
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>>
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623