[gmx-users] Amino terminus atom types
Lieven Buts
lieven at ultr.vub.ac.be
Mon Dec 1 10:33:01 CET 2003
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
More information about the gromacs.org_gmx-users
mailing list