leila karami wrote:
Hi
1) what means of option -ter in pdb2gmx command?
The option allows you to set the protonation state.
2) I simulate protein-dna complex and I put N and C terminal as NH3+ and
COO-, respectively for obtaining zwitterionic condition.
what is difference between 1 and 2
The difference should be fairly obvious, based on the nomenclature printed by
pdb2gmx. For N-termini, choice 1 is NH3+ and 2 is NH2, and analogously for the
C-terminus. The default is charged, so if you want charged termini, you don't
need to be using the -ter flag.
-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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