[gmx-users] Amino terminus atom types
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 1 11:50:02 CET 2003
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:
> > > [ 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
> > ...
> > > ----------------------------
> > > run, I get these LINCS warnings:
> > 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
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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