[gmx-users] Amino terminus atom types

[David van der Spoel]

On Mon, 2003-12-01 at 10:31, Lieven Buts wrote:
> 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).
In that case, yes, pdb2gmx can not treat this kind of oddities. You will
have to make a new glutamine residue entry in the rtp file (and hdb
file).

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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