balaji nagarajan wrote:
Dear Users !
i have tried in generating the -ter option in generating the topology
file !
it asks the below if i give the ter option ,
Select start terminus type for TYR-1
0: NH3+
1: ZWITTERION_NH3+
2: NH2
3: None
then if i give option 1 it chooses ZWITTERION_NH3+ , i want to make
the charge state of the protein as ZWITTERION , in terminal how to do
it in command mode
The zwitterion option should only be invoked in the case of a single,
zwitterionic amino acid. For any polypeptide you should choose normal termini
(NH3+ and COO- in your case). If you choose the zwitterion forms, your topology
will be broken.
-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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