[gmx-users] Parametrisation of the heteroatomic pdb
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Oct 29 12:38:07 CEST 2011
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 <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
>
> 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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