[gmx-users] Amino terminus atom types

[Lieven Buts]

On Thursday 20 November 2003 14:26, David van der Spoel wrote:
> On Thu, 2003-11-20 at 13:55, Lieven Buts wrote:
> > I am trying a simple simulation of a protein in water using the OPSL-AA
> > force field in Gromacs 3.1.4. The N terminus looks like this in the
> > topology file:
<snip>
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass 
> > typeB chargeB      massB
> >      1       MNH3      1    GLN    MN1      1          0    8.51535
> >      2       MNH3      1    GLN    MN2      1          0    8.51535
<snip>
> ...
> > ----------------------------
<snip>
> > run, I get these LINCS warnings:
<snip>
> yes,
>
> I'm working on it.
>
> > Cheers,

Could the problem be specific for this protein? I am asking because the 
starting model is based on our crystal structure of the protein, and the 
electron density clearly indicated that the N-terminal glutamine is cyclic 
(by reaction of the side chain with the main chain).

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel