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

[kinshuk at chem.iitb.ac.in]

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.

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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