[gmx-users] pdb2gmx -ter

[Milan Melichercik]

On Pi 9. Júl 2004 12:09, Raghunadha Reddy Burri wrote:
> Dear GMX users,
>
> I have a small question,
>
> I have a peptide WITHOUT any N & C terminus but I want simulate with  N & C
> terminus "ACE - peptide - NME"
>
> When I using
>
> pdb2gmx -f -ter -ignh
>
> 3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>
> Select N-terminus type (start)
>  0: NH3+
>  1: ZWITTERION_NH3+
>  2: NH2
>  3: None

IMHO it depends on environment properties (pH), if you have/need -NH2 group or  
ionised -NH3+ (or something between them).
The 4th choice leave your pepride without change and that is what you don't 
want.

Milan