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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Received on Tue Mar 21 2023 - 09:30:04 PDT
