[gmx-users] terminal_fixing

[Justin A. Lemkul]

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

-- 
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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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