Re: [AMBER] problem with antechamber

From: Maryam Hamzehee <maryam_h_7860.yahoo.com>
Date: Wed, 28 Jan 2015 11:45:46 +0000 (UTC)

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 _______________________________________________ AMBER
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> >   
>
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Received on Wed Jan 28 2015 - 04:00:02 PST
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