[gmx-users] Intermolecular Distance Restraints

Berk Hess gmx3 at hotmail.com
Fri Aug 13 09:45:02 CEST 2004

>From: "Warren DeLano" <warren at delanoscientific.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] Intermolecular Distance Restraints
>Date: Thu, 12 Aug 2004 20:43:22 -0700
>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 
>a proper pdb2gmx topology with proper termini, it seems that the enzyme &
>substrate need to be separate molecules.
>2) According to some prior posts on the list, there is no way in GROMACS to
>define the topology for intermolecular distance restraints.
>I'm stuck.  Is there a general way around this?  If not, then what's the
>least painful workaround?

pdb2gmx -merge does what you want, although the description is not very 
I have added intermolecular distance restraints to the pdb2gmx -h help,
since more questions have been asked about this on the list.


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