[gmx-users] extra-bond

[Stefano Guglielmo]

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
>
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-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178