[gmx-users] Intermolecular Distance Restraints
spoel at xray.bmc.uu.se
Sun Aug 15 11:49:14 CEST 2004
On Sun, 2004-08-15 at 07:24, Kay Gottschalk wrote:
> It would be great to teach PyMol how to read Gromacs!
> On Aug 13, 2004, at 6:43 AM, Warren DeLano wrote:
> > Hello,
> > I've finally learning some GROMACS and have been using it to
> > model/refine
> > some enzyme-substrate complexes. I'd like to be able to build some
> > arbitrary distance constraints into the simulation, but that is
> > starting to
> > look like a problem. Here's the deal:
> > 1) I've got two chains with different termini -- the enzyme needs to be
> > NH3+/COO-, but the substrate should be capped ACE/NAC. In order to
> > generate
> > a proper pdb2gmx topology with proper termini, it seems that the
> > enzyme &
> > substrate need to be separate molecules.
Don't know whether this has been answered before: you need to give them
different chain identifiers, and then pdb2gmx will ask you about the
termini (maybe you need -ter option)
> > 2) According to some prior posts on the list, there is no way in
> > GROMACS to
> > define the topology for intermolecular distance restraints.
Yes, it should work with using pdb2gmx -merge.
> > I'm stuck. Is there a general way around this? If not, then what's
> > the
> > least painful workaround?
> > Would it be worthwhile teaching PyMOL how to visualize, manipulate, &
> > merge
> > GROMACS topologies?
David van der Spoel, PhD, Assoc. 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
More information about the gromacs.org_gmx-users