[gmx-users] Intermolecular Distance Restraints

[David]

On Sun, 2004-08-15 at 07:24, Kay Gottschalk wrote:
> It would be great to teach PyMol how to read Gromacs!
> K.
> 
> 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?
Definitely... 
-- 
David.
________________________________________________________________________
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
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