nishap.pa...@utoronto.ca wrote:
Hello,
I want to simulate n-glycines (diglycine, triglycine..etc) I tried to
get the structure from PRODRG, but the program adds H's on the
N-terminal instead of on C- terminal. Is there another program I could
use, or a site where I could get the structure of oligoglycines? For
example, diglycine (NH2-CH2-CO-NH-CH2-COOH), but PRODRG gives me
((NH3-CH2-CO-NH-CH2-COO)
Protonation state is easy to change with pdb2gmx when writing your topology.
Use -ignh and/or -ter to set the proper state. You can also tune this with
PRODRG (see the FAQs regarding ADDHYD and DELHYD commands), but since you can do
it all with Gromacs anyway, it shouldn't be necessary.
-Justin
Thanks!
Nisha P
--
========================================
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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