[gmx-users] rtp

Xavier Periole X.Periole at rug.nl
Sat Dec 15 11:38:55 CET 2007

On Fri, 14 Dec 2007 14:27:10 -0800
  Arthur Roberts <aroberts99163 at yahoo.com> 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".


> 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

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