[gmx-users] generation of guanidium intramolecular force-field

[David van der Spoel]

kinshuk at chem.iitb.ac.in wrote:
> Thanks for providing the insight about it. I have tried it.
> I have two query..
> (1) As in the case of simulation with urea as a solute and water as
> solvent the corresponding file urea+h2o.gro file is given there.I have to
> do simulation similar to urea i.e. guanidium ion as a solute in place of
> urea.So in that case how will i be able to create Gdm+h2o.gro file
> analogous to urea+h2o.gro(Gdm=Guanidium ion).
> 
> (2) If i have to perform simulation with varying concentration of
> system(Guanidium & water), so how will i be able to do it.As i have seen
> in case of urea+h2o.gro concentration of system is fixed and if i have to
> generate a system of different molal(different ratio of urea and water),
> so will be play with concentration.
> 
> If any help i will be getting, i will be very thankful.
> 
genconf + genbox

> kinshuk raj srivastava
> IIT-Bombay
> India
> 
> 
> 
> 
>  Quoting kinshuk at chem.iitb.ac.in:
>>>
>>> Hi all,
>>>   I have been try to put up MD simulation of guanidium chloride
>>> simulation
>>> in SPC water model.I have been facing problem regarding *.rtp, *.itp
>>> file generation for new entry for guanidium ion.If any one is aware
>>> about how to create above mentioned file please let me give some insight
>>> about file corresponding guanidium ion.
>>>   I tried to make it with argenine side chain but i have been facing
>>> problem while generating above mentioned file.
>> http://wiki.gromacs.org/index.php/Parameterization
>>
>> You could use PRODRG to generate the topology, but you will have to
>> validate the
>> parameters (see the above link), especially the charges that PRODRG
>> assigns.
>> They are often unsatisfactory.
>>
>> -Justin
>>
>>>
>>> kinshuk raj srivastava
>>> IIT-Bombay
>>> Mumbai, India
>>>
>>>
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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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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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