On 29/10/2011 7:38 PM, James Starlight wrote:
Mark, hello!
It's clear now about termii
also I'd like to know about orientation of my protein along specific axis
e.g editconf -princ orient my protein along X but what should i do to
orient it along other axis?
Did you start by trying to look up the answer in editconf -h yourself?
Mark
James
2011/10/29 Mark Abraham <[email protected]
<mailto:[email protected]>>
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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