Chandan Choudhury wrote:
Hello gmx-users
I am trying to simulate an amino acid (say GLN). It can be as a
zwitterionic form or uncharged ends. Neither ffamber or ffopls force
fields has a complete parameter for them. While in ffamber, I have the
This is not true. OPLS can handle isolated amino acids, you just have to
manually choose the termini in pdb2gmx (using -ter). Use the "zwitterion" forms
of the termini, since in fact, you have a zwitterion.
-Justin
parameters for CGLU and NGLU, but not for a Glutamine. Do I need to
define it there, or there is some way out. If I need to define it, how
do I retrive the partial charges.
Any insight would be very helpful.
Thanks
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
========================================
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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