[gmx-users] Parametrisation of the heteroatomic pdb

Mark Abraham Mark.Abraham at anu.edu.au
Sat Oct 29 09:53:29 CEST 2011

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 ?


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