[gmx-users] regarding rtp file

[Justin A. Lemkul]

priya thiyagarajan wrote:
> hello sir,
>  Thanks for your reply..
> i like to know is it better to do x2top for my whole protein instead of 
> seperating fattyacid from aminoacid to generate rtp file and top file 
> since  mine is a cyclicheptapeptide..
> so that i can use that top file for doing my energy minimization 
> ,position restr ad dynamics..
> 

The best tool for this job is pdb2gmx; g_x2top only works well for single small 
molecules, not the complex multi-residue species you're dealing with.  Not only 
will pdb2gmx write the appropriate topology for the peptide, but it will allow 
you to deal with special bonds and termini that may be required for building the 
cyclic peptide.  See also:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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