[gmx-users] regarding x2top

[Justin A. Lemkul]

priya thiyagarajan wrote:
> 
> 
> 
> hello sir,
>  thanks for your  reply..
>  The thing is i seperated my  fattyacid portion from aminoacid..
> so carbon missing its bond.
> That 1st carbon linked to c, one double bonded o and glu aminoacid...
> how i need to model my input..
> shall i need to draw my fattyacid portion alone in chemsketch and then 
> have to use it as input in x2top..
> help me with your answer sir..
> 

If this residue is chemically connected to an amino acid in the protein, then 
having an independent topology via g_x2top does you no good.  The better 
approach is to create an .rtp entry for the glutamate/fatty acid conjugate.

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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