Dear Friends,
Thank you very much for your kind suggestions!
Indeed this was an issue in my preparation setup using antechamber, which
took both residues at the same time.
BTW, I have a question related to the analysis of the system containing two
identical ligands (the both named as LIG) bound in two different monomers
of the complex. How could it be better to specify the atom mask
corresponding to a specific ligand (e.g. for mmgbsa) ? The only one
solution could be based only on the residue name in this case ?
Many thanks in advance !
Yours sincerely
Enrico
Il giorno mar 21 mar 2023 alle ore 17:27 Dr. Anselm Horn via AMBER <
amber.ambermd.org> ha scritto:
> Dear Enrico,
>
> it is not clear to me what you are doing:
> If you already have the parameters for your ligand, then you need to
> load them only once into leap; the programs identifies the ligand
> according to its residue name, and thus it can deal with several
> identical residues in your (pdb) input, as long as the residue names in
> your input and the parameter files do match.
>
> If you are still in the parameterization phase, then you also need only
> one instance of your ligand.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 21.03.2023 um 17:00 schrieb Enrico Martinez via AMBER:
> > Dear Amber Users !
> >
> > I have an issue related to the preparation of the system containing two
> > identical ligands present in two different binding sites. Actually when I
> > try to copy the both units for the parametrization using Antechamber it
> > says that it could not process two residues at the same time.
> >
> > Is there any preparation trick for such a case assuming that everything
> > works fine with the same system containing only one ligand ?
> >
> > Many thanks in advance
> >
> > Enrico
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> >
>
>
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Received on Thu Mar 23 2023 - 05:30:03 PDT
