On Fri, 14 Dec 2007 14:27:10 -0800
Arthur Roberts <[EMAIL PROTECTED]> wrote:
Dear Jayant,
I might be wrong, but I think the original gmx force field that you are
referring to has been deprecated.
This is correct. It is better to use the OPLS FF if you like to include
hydrogens in your description of the protein. You also have the option
to run with the GROMOS FF and then add the proton with "protonate".
XAvier
Best wishes,
Art
On Dec 14, 2007, at 1:44 PM, jayant_jacques wrote:
Hi!
I am attempting to simulate a protein with a modified amino acid
using the Gromacs force field with hydrogens for NMR. I have built
the RTP and TOP files using PRODRG.
I need to know what is the rtp file? relevant to the above force
field such that I can append my rtp file. Is it the ffgmx2.rtp or
ffgmx.rtp?
Thanks
Jayant James
Jayasundar Jayant James
Postdoc,
Department of Veterinary and Comparative Anatomy, Pharmacology and
Physiology(VCAPP), Washington state university, Pullman 99164-6520,
USA.
http://www.chick.com/reading/tracts/0001/0001_01.asp
Phone office:335-5937, Cell:1-509-432-5790
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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