[gmx-users] extra-bond

[Mark Abraham]

Hi,

Look for [ intermolecular_interactions ] in the manual!

Mark

On Sun., 10 Mar. 2019, 11:23 Stefano Guglielmo, <stefano.guglielmo at unito.it>
wrote:

> Thanks for quick reply Justin; as the atom pairs come from two molecules,
> is pdb2gmx the only way to merge different molecules in a single [
> moleculetype ]? I got some troubles with it supposingly because the system
> was generated with Ambertools and then converted, thus pdb2gmx does not
> recognize properly all the residues.
>
> Thanks again
> Stefano
>
> Il giorno sab 9 mar 2019 alle ore 22:58 Justin Lemkul <jalemkul at vt.edu> ha
> scritto:
>
> >
> >
> > On 3/9/19 12:23 PM, Stefano Guglielmo wrote:
> > > Dear gromacs users,
> > > I have a system with a topology generated from Amber and then converted
> > > through ParmEd into gromacs-formatted stuff. I would like to add
> distance
> > > restraints for several pairs of atoms (ca 20). Is it possible to add
> them
> > > with grompp or should I edit the .top file some way?
> >
> > Distance restraints need to be defined in the topology.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
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