The attached PDB already has all hydrogens added. Reduce won't add
anything (and that what it tells you) because there is nothing to add.
The problem is eventually antechamber getting confused with the CONECT
records in your PDB. Add -j 4 to your call to antechamber and it will
ignore those records.
antechamber -i catechin-over.pdb -fi pdb -o cat.mol2 -fo mol2 -c bcc -s
2 -j 4
Alternatively, delete them from the PDB.
Cheers,
Hannes.
On Wed, 28 Jan 2015 09:40:58 +0000
Maryam Hamzehee <maryam_h_7860.yahoo.com> wrote:
> Many thanks for the email, I tried to add hydrogens via reduce
> command but the hydrogens were not added! The following error is
> observed while running the command:
>
>
>
> [maryam.cluster catechin]$ reduce catechin-over.pdb >
> catechin-over-h.pdbreduce: version 3.14 08/21/2008, Copyright
> 1997-2008, J. Michael WordProcessing file:
> "catechin-over.pdb"Database of HETATM connections:
> "/share/apps/amber11//dat/reduce_wwPDB_het_dict.txt"Processing only
> 'A' conformations.VDW dot density = 16/A^2Orientation penalty scale =
> 1 (100%)Eliminate contacts within 3 bonds.Ignore atoms with
> |occupancy| <= 0.01 during adjustments.Waters ignored if B-Factor >=
> 40 or |occupancy| < 0.66Aromatic rings in amino acids accept hydrogen
> bonds.Building or keeping OH & SH Hydrogens.Rotating NH3
> Hydrogens.Processing Met methyls.WARNING: atom H171 from LIG will be
> treated as hydrogenWARNING: atom H171 from LIG will be treated as
> hydrogenWARNING: atom H172 from LIG will be treated as
> hydrogenWARNING: atom H172 from LIG will be treated as
> hydrogenWARNING: atom H171 from LIG will be treated as
> hydrogenWARNING: atom H172 from LIG will be treated as
> hydrogenWARNING: atom HC10 from LIG will be treated as
> hydrogenWARNING: atom HC10 from LIG will be treated as
> hydrogenWARNING: atom HC13 from LIG will be treated as
> hydrogenWARNING: atom HC13 from LIG will be treated as
> hydrogenWARNING: atom HC15 from LIG will be treated as
> hydrogenWARNING: atom HC15 from LIG will be treated as
> hydrogenWARNING: atom HC22 from LIG will be treated as
> hydrogenWARNING: atom HC22 from LIG will be treated as
> hydrogenWARNING: atom HC24 from LIG will be treated as
> hydrogenWARNING: atom HC24 from LIG will be treated as
> hydrogenWARNING: atom HC26 from LIG will be treated as
> hydrogenWARNING: atom HC26 from LIG will be treated as
> hydrogenWARNING: atom HC28 from LIG will be treated as
> hydrogenWARNING: atom HC28 from LIG will be treated as hydrogenFound
> 14 hydrogens (14 hets)Standardized 0 hydrogens (0 hets)Added 0
> hydrogens (0 hets)Removed 0 hydrogens (0 hets)If you publish work
> which uses reduce, please cite:Word, et. al. (1999) J. Mol. Biol.
> 285, 1735-1747.For more information see
> http://kinemage.biochem.duke.edu
>
> All the bestMaryam My ligand is attached.
>
>
>
> On Wednesday, 28 January 2015, 11:40,
> "hannes.loeffler.stfc.ac.uk" <hannes.loeffler.stfc.ac.uk> wrote:
>
> Before you hand the structure to antechamber you will have to make
> sure to have all atoms, in particular the hydrogens, added. You also
> need to be clear about the total charge of your molecule.
>
> ________________________________________
> From: Maryam Hamzehee [maryam_h_7860.yahoo.com]
> Sent: 28 January 2015 06:27
> To: amber list
> Subject: [AMBER] problem with antechamber
>
> Dear Amber List
> I am one of AMBER users, I am trying to do energy minimization and MD
> simulation for my ligand-receptor complex. I had a look to the
> tutorial http://ambermd.org/tutorials/basic/tutorial4b/, but when I
> was doing this tutorial for my molecule, it didn't work. I generated
> the small molecule in hyperchem and did energy minimization and did
> overly of the molecule using Pymol. But the reduce and
> antechambercommand did not work in my system. Reduce command did not
> add hydrogens but generated the structure and when I ran antechamber
> command the following error is appeared:
>
> [maryam.cluster catechin]$ antechamber -i catechin-over-h.pdb -fi pdb
> -o cat.mol2 -fo mol2 -c bcc -s
> 2Running: /share/apps/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Warning:
> the assigned bond types may be wrong, please : (1) double check the
> structure (the connectivity) and/or (2) adjust atom valence penalty
> parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and
> recompile bondtype.c Be cautious, use a large value of PSCUTOFF
> (>100) will significantly increase the computation time Error: cannot
> run "/share/apps/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit[maryam.cluster
> catechin]$ I used openbabel, SPDBV, Pymol for changing the file
> format but none of them did work. I would be grateful if you help me
> in this regard. Your reply would be highly appreciated. All the
> bestMaryam _______________________________________________ AMBER
> mailing list AMBER.ambermd.org
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Received on Wed Jan 28 2015 - 02:00:04 PST
