[gmx-users] Parametrisation of the heteroatomic pdb

[James Starlight]

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?

James

2011/10/29 Mark Abraham <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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