[gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

[Alessandra Villa]

Hi,
I meant to use the option of "-merge" of pdb2gmx, to generate one file for
protein + ligands (top)
Best regards
Alessandra

On Fri, Dec 13, 2019 at 11:44 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Thank you, Alessandra, for your reply.
>
> I have a confusion here that when I merge the topology I will have to
> reindex ligand atoms. *e.g *I have ligand topology starting with atom
> number 1 and bond terms, angles, dihedrals have all the connectivity
> numbering from 1 to so on.  When I will change the index number in combined
> topology; will it not affect these terms? Could you please explain a bit
> more? I have attached a ligand file for reference.
> Thanks in advance.
>
> Sadaf
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