On Thu, Sep 17, 2015, Atila Petrosian wrote:
>
> $AMBERHOME/exe/reduce lig.pdb > lig_h.pdb
Reduce uses a library of common ligands to know where to place hydrogens:
>
> Database of HETATM connections:
> "/home/linux/Desktop/amber/amber11/dat/reduce_wwPDB_het_dict.txt"
If you just name your ligand "LIG", reduce won't be able to help. If this
really came from a pdb entry, us the residue name in the PDB entry: that is
what reduce knows about.
> Processing Met methyls.
> WARNING: atom H171 from LIG will be treated as hydrogen
??? Looks like you gave it a pdb file with more than just the ligand(?).
I don't see any warnings like this when I run reduce on your "lig.pdb" file.
>
> Is there another way to addidng H atoms to my ligand?
Just draw them in by hand in xleap or some other graphical program. That's
a simple one-off solution. People on the list might chime in here with
their favorite way to add hydrogens.
....dac
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Received on Thu Sep 17 2015 - 12:00:03 PDT
