[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Sat Oct 29 09:34:32 CEST 2011

Justin, hello!

I've desided to make simulation of my GA peptide under GROMOS96 53A6 force
field extended with Berger lipids ( on analogy to KALP simulation because
both of that lipids are membrane alpha helices with similar topology )

About termii- As I understood you've added ACE and NH2 termii to KALP via
Amber tools software. I havent that software now but pdb2gmx under GROMOS96
53A6 force field may add only NH(2) cap to the C-end and COO(H) to the N-end
instead of ACE and NH2.

Identified residue VAL2 as a starting terminus.
Identified residue TRP16 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-2
 0: NH3+
 1: NH2
 2: None

It's not quite unferstand for me why pdb2gmx add the termii in such wrong
manner ( e.g ACE and other groups also contains in the .rtp of this ff).
Finally why I cant chose NH(2) for the last residue and the COOH for the
first ? And what difference beetwen such termii specification would be as
the consequence ?

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