On 29/10/2011 6:34 PM, James Starlight wrote:
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.
I can't understand any of that :)
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).
Termini are added by pdb2gmx using the terminus databases in the .n.tdb
and .c.tdb files, as you would know from your reading of chapter 5 of
the manual :-) Only things that are found there can be added by pdb2gmx
- and not everything you can imagine will be found there. If you want
(for example) an ACE group at your N-terminus, you need to build it
using some other tool, and arrange for the .rtp entry for ACE to exist
(which it already does).
Finally why I cant chose NH(2) for the last residue and the COOH for
the first ?
Because they've either not been parameterized, coded or tested.
And what difference beetwen such termii specification would be as the
consequence ?
Mark
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