Dear Hannes
Thanks a lot. The problem was fixed.
Cheers,Maryam
On Wednesday, 28 January 2015, 15:22, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
You need to keep the hydrogens but not the connections.
On Wed, 28 Jan 2015 11:45:46 +0000
Maryam Hamzehee <maryam_h_7860.yahoo.com> wrote:
> Dear Hannes
> I removed all the hydrogens as well as connections but unfortunately
> it did not work as I tried all of them before. The problem is still
> existing. Here is the following error: [maryam.cluster catechin]$
> antechamber -i catechin-over_h.pdb -fi pdb -o cat.mol2 -fo mol2 -c
> bcc -s 2 Running: /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]$ antechamber -i catechin-over_h.pdb -fi pdb -o cat.mol2 -fo
> mol2 -c bcc -s 2 Running: /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]$
>
> Many thanks
> Maryam
> P.S. The edited file (without hydrogens) is attached.
>
>
>
> On Wednesday, 28 January 2015, 13:34, Hannes Loeffler
> <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> Sorry, -j 4 won't help (I guess its the default anyway). Just delete
> the CONECT records in the PDB.
>
>
> On Wed, 28 Jan 2015 09:58:16 +0000
> Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> > 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 _______________________________________________
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> >
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Received on Wed Jan 28 2015 - 05:30:07 PST
