On Mon, Mar 20, 2017, Nirupma Singh wrote:
> I am trying to add hydrogens to my ligand file using reduce command in
> amber but it is not adding any hydrogen to the ligand.
> Database of HETATM connections:
> "/opt/apps/amber14/dat/reduce_wwPDB_het_dict.txt"
Reduce only knows about the ligands that are present in its database
(above), which covers those ligands in the PDB repository. It is not a
general-purpose program that can deal with arbitrary ligands, and it doens't
know what to do with your molecule named "lig".
You will need to either figure out what the PDB-standard name is for your
ligand, and use other software, not present in AmberTools.
...good luck...dac
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Received on Mon Mar 20 2017 - 05:30:04 PDT
