Thanks Justin!
Nisha P
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] 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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