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
--
========================================
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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