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

[Justin A. Lemkul]

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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