[gmx-users] -ter in pdb2gmx

[Justin A. Lemkul]

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

-- 
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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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