Re: [AMBER] problem with antechamber

From: Maryam Hamzehee <maryam_h_7860.yahoo.com>
Date: Wed, 28 Jan 2015 09:40:58 +0000 (UTC)

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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Received on Wed Jan 28 2015 - 02:00:03 PST
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