Preparing Zinc Ligand Database For Screening With Am1Bcc Charges
Hi, I want to screen a large ZINC database for ligands that fit in an enzyme active site. I have setup the SLIDE software to do this task for ligands in mol2 format. I assigned AM1BCC charges with Chimeras addcharge before, which worked fine.
When I try to add charges to a ZINC database mol2 file it will always end up with various error messages. I could make it work with 2 or 3 ligands but never with more than 3 ligands in a mol2 file.
Does anyone know how to add AM1BCC charges to a ZINC database file with more than 100 ligands?
Thanks guys!
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Examples of the "various error messages"?
Last time I tried, I got this:
No incomplete side chains Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: Hydrogens added Charge model: AMBER ff12SB No incomplete side chains Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Charge model: AMBER ff12SB Assigning partial charges to residue <0> (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/antechamber -ek qm_theory='AM1', -i /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpp1DWbm/ante.in.mol2 -fi mol2 -o /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpp1DWbm/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (<0>)
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(<0>) Total number of electrons: 194; net charge: 0
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/Chimera.app/Contents/Resources/bin/amber12/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(<0>)
Charges for residue <0> determined Assigning partial charges to residue <0> (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/antechamber -ek qm_theory='AM1', -i /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmp9copWG/ante.in.mol2 -fi mol2 -o /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmp9copWG/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (<0>)
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(<0>) Total number of electrons: 128; net charge: 1
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/Chimera.app/Contents/Resources/bin/amber12/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(<0>)
Charges for residue <0> determined Assigning partial charges to residue <0> (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/antechamber -ek qm_theory='AM1', -i /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpnC5byh/ante.in.mol2 -fi mol2 -o /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpnC5byh/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (<0>)
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(<0>) Total number of electrons: 102; net charge: 0
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/Chimera.app/Contents/Resources/bin/amber12/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(<0>)
Charges for residue <0> determined Assigning partial charges to residue <0> (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/antechamber -ek qm_theory='AM1', -i /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpV__ox9/ante.in.mol2 -fi mol2 -o /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpV__ox9/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (<0>)
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(<0>) Total number of electrons: 156; net charge: 0
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/Chimera.app/Contents/Resources/bin/amber12/dat/antechamber/BCCPARM.DAT -s 2 -j 1
(<0>)
Charges for residue <0> determined Assigning partial charges to residue <0> (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/antechamber -ek qm_theory='AM1', -i /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpDI8tXw/ante.in.mol2 -fi mol2 -o /var/folders/58/6gxw74td4yz4n6tp8qrnljy40000gn/T/tmpDI8tXw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(<0>) Total number of electrons: 193; net charge: 1
(<0>) INFO: Number of electrons is odd: 193
(<0>) Please check the total charge (-nc flag) and spin multiplicity (-m flag)
(<0>)
(<0>) Running: /Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out
(<0>) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber12/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
Failure running ANTECHAMBER for residue <0> Check reply log for details