[gmx-users] Parametrisation of the heteroatomic pdb

[Mark Abraham]

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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