Re: [AMBER] antechamber error

From: David A Case <david.case.rutgers.edu>
Date: Thu, 17 Sep 2015 14:47:15 -0400

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 17 2015 - 12:00:03 PDT
Custom Search