[gmx-users] Protein Solvent Dynamics - Coordinates for docking

[ram bio]

Dear Justin,

Thanks for the advice, will try to follow using grace.

Ram

On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin.
>>
>> Thanks for the suggestion, definitely i would run next time for a
>> longer time 2-10 ns.
>> Here, I want to learn the analysis part of the mdrun, In order to
>> locate the lowest energy frame  I executed command g_energy -f
>> md_0_1.edr -o PE.xvg and the output was
>>
>> Statistics over 500001 steps [ 0.0000 thru 1000.0001 ps ], 1 data sets
>> All averages are exact over 500001 steps
>>
>> Energy                      Average       RMSD     Fluct.      Drift
>>  Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Potential                -1.2189e+06    1115.54    1070.01    -1.0927
>>  -1092.7
>>
>> then I had a look at the PE.xvg file, but the values are very close to
>> identify the lowest energy point, i also tried to a have a look at the
>> md_0_1.log file, here also it is tedious and time consuming and the
>> values are close to remember. Can you suggest me how to locate the
>> lowest energy frame, so that i can use the comand (below) to retrieve
>> that particular frame coordinates in PDB file:
>>
>
> I would suggest writing a script.  I think plotting tools like Grace can
> also extract minimum values from data sets.  If the values are so close
> together, then ask yourself whether the lowest of these values is
> significantly different from any of the other conformation.  Also, an RMSD
> analysis will tell you how much the structure has changed (or is changing).
>
>> trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame
>> number- corresponding to the lowest energy)
>>
>>
>> and also please tell the whether the command i am going to use to
>> retrieve the lowest energy configuration is correct.
>
> Close.  You also need to use -s when interconverting formats (I believe),
> and -dump is not given a frame number, but rather a time in ps.
>
>>
>> Thanks,
>>
>> Ram
>>
>>
>> On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> ram bio wrote:
>>>>
>>>> Dear Justin,
>>>>
>>>> Thanks for the suggestion and advice.
>>>> As i have used a modelled protein and want to obtain the lowest energy
>>>> configuration of the protein by doing dynamics, i want to collect the
>>>> structure (coordinates in pdb) representing average of all the
>>>> frames/configurations produced in MD and also the lowest energy
>>>> configuration structure (coordinates in PDB) produced during the
>>>> simulation, which can be used for docking. Please help how to obtain
>>>> the average structure as well as the lowest energy configuration
>>>> structure.
>>>>
>>> Average structures are not always meaningful (or even
>>> physically-relevant):
>>>
>>> http://www.gromacs.org/Documentation/Terminology/Average_Structure
>>>
>>> You can get average structures from, i.e. g_cluster -cl, if you want.  As
>>> for the lowest energy structure, analyze potential energy, and dump out
>>> the
>>> frame corresponding to the lowest point.  Hopefully you saved coordinates
>>> and energies at the same interval :)  The potential energy will
>>> correspond
>>> to that of the system, but hopefully it should give some indication of
>>> the
>>> lowest energy configuration.  I don't know anything about your system,
>>> but
>>> it will also depend on how much the energy fluctuates as to how relevant
>>> this structure might be, and how different it might be from an "average."
>>>
>>> If your structure comes from some model you built, realize that 1 ns is
>>> an
>>> exceptionally short time frame, especially given the capabilities of
>>> modern
>>> hardware and the speed of the GROMACS code.  You may want to consider
>>> running a bit longer to ensure that you really have a stable system.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> 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
>
> ========================================
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