Hi Karan
Did u renamed Cystein present in your protein that is making bond.??
hope it would be the problem.
On Fri, Dec 10, 2010 at 7:08 AM, Karan Mehra <kkm7r.virginia.edu> wrote:
> Hello Amber Experts,
>
> I am trying to prepare amber input files for HORSE HEART CYTOCHROME
> C<http://www.pdb.org/pdb/files/1HRC.pdb>.
> I keep running into error messages that I believe deal with the
> heme_all.inand frcmod
> .heme files. I recently searched the previous messages in the mailing list
> to look for solutions but I found no luck. Here is what I did:
>
> -I downloaded the heme_all.in and heme.frcmod files from
> http://www.pharmacy.manchester.ac.uk/bryce/amber.
> -I edited these files according to the following suggestions found in a
> previous email thread:
>
> *(Issue #1) Add the following lines to the nonbonded (bottom) section
> of the frcmod file:
> NO 1.8240 0.1700 OPLS
> NP 1.8240 0.1700 OPLS
> CX 1.9080 0.0860 Spellmeyer
>
> From looking at older parm*.dat files, these are the correct intended
> parameters for these atom types.
>
>
> (Issue #2) Move the partial charges from the bottom section of the
> prep file to being the right-most column of the top section, e.g.:
>
> 0 0 2
> *
> *
> Heme residue ALL ATOM, Yves names, Bayly-modified
> *
> *heme_all.db3
> HEM INT 0
> CORRECT OMIT DU BEG
> 0.50000
> 1 DUMM DU M 0 0 0 0.0000 0.0000
> 0.0000 0.0000
> 2 DUMM DU M 1 0 0 1.4490 0.0000
> 0.0000 0.0000
> 3 DUMM DU M 2 1 0 1.5220 111.1000
> 0.0000 0.0000
> 19 FE FE M 16 14 12 2.1000 124.0000
> 180.0000 0.2500
> 20 NA NP S 19 16 14 2.0800 98.0000
> 90.0000 -0.1800
> ... and so forth ...*
>
> *- *I have attached the edited heme_all.in and frcmod.heme files
>
> Here are the error messages which I am receiving:
> [kkm7r.helium HEME]$ tleap
> -I: Adding /itc/common/amber/10/amber10/dat/leap/prep to search path.
> -I: Adding /itc/common/amber/10/amber10/dat/leap/lib to search path.
> -I: Adding /itc/common/amber/10/amber10/dat/leap/parm to search path.
> -I: Adding /itc/common/amber/10/amber10/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /itc/common/amber/10/amber10/dat/leap/cmd/leaprc.ff99SB
> done
> Log file: ./leap.log
> Loading parameters: /itc/common/amber/10/amber10/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters:
> /itc/common/amber/10/amber10/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library:
> /itc/common/amber/10/amber10/dat/leap/lib/all_nucleic94.lib
> Loading library: /itc/common/amber/10/amber10/dat/leap/lib/all_amino94.lib
> Loading library:
> /itc/common/amber/10/amber10/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /itc/common/amber/10/amber10/dat/leap/lib/all_aminont94.lib
> Loading library: /itc/common/amber/10/amber10/dat/leap/lib/ions94.lib
> Loading library: /itc/common/amber/10/amber10/dat/leap/lib/solvents.lib
> > loadamberparams frcmod.hemall
> Loading parameters: ./frcmod.hemall
> Reading force field modification type file (frcmod)
> Reading title:
> Force field modifcations for all-atom heme
> > loadamberprep heme_all.in
> Loading Prep file: ./heme_all.in
> Warning: per-line charges being overridden by CHARGE block in Heme
> residue ALL ATOM, Yves names, Bayly-modified
> > prot = loadpdb /home/kkm7r/pdb/cyt.pdb
> Loading PDB file: /home/kkm7r/pdb/cyt.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C4D-ND-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C1D-ND-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CAC-CBC-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-CAB-CBB-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C4B-NB-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C1B-NB-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-FE-NB-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-FE-ND-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> total atoms in file: 869
> Leap added 880 missing atoms according to residue templates:
> 880 H / lone pairs
> > saveamberparm prot cyt.prmtop cyt.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - CY
> Could not find bond parameter for: SH - CY
> Could not find bond parameter for: NA - FE
> Could not find bond parameter for: S - FE
> Building angle parameters.
> Could not find angle parameter: HS - SH - CY
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: HS - SH - CY
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: CW - NA - FE
> Could not find angle parameter: H - NA - FE
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - S
> Could not find angle parameter: CR - NA - FE
> Could not find angle parameter: CT - S - FE
> Could not find angle parameter: S - FE - NP
> Could not find angle parameter: S - FE - NO
> Could not find angle parameter: S - FE - NP
> Could not find angle parameter: S - FE - NO
> Could not find angle parameter: CT - S - FE
> Building proper torsion parameters.
> ** No torsion terms for HS-SH-CY-CB
> ** No torsion terms for HS-SH-CY-HC
> ** No torsion terms for HS-SH-CY-CX
> ** No torsion terms for CT-SH-CY-CB
> ** No torsion terms for CT-SH-CY-HC
> ** No torsion terms for CT-SH-CY-CX
> ** No torsion terms for HS-SH-CY-CB
> ** No torsion terms for HS-SH-CY-HC
> ** No torsion terms for HS-SH-CY-CX
> ** No torsion terms for CT-SH-CY-CB
> ** No torsion terms for CT-SH-CY-HC
> ** No torsion terms for CT-SH-CY-CX
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-S
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-S
> ** No torsion terms for NA-FE-S-CT
> ** No torsion terms for NA-FE-S-CT
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-S
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> ** No torsion terms for CT-S-FE-NP
> ** No torsion terms for CT-S-FE-NO
> Building improper torsion parameters.
> old PREP-specified impropers:
> <HEM 105>: NA C1A C4A FE
> <HEM 105>: NB C1B C4B FE
> <HEM 105>: NC C1C C4C FE
> <HEM 105>: ND C1D C4D FE
> <HEM 105>: C1A C2A NA CHA
> <HEM 105>: C1B C2B NB CHB
> <HEM 105>: C1C C2C NC CHC
> <HEM 105>: C1D C2D ND CHD
> <HEM 105>: C2A C3A C1A CAA
> <HEM 105>: C2B C3B C1B CMB
> <HEM 105>: C2C C3C C1C CMC
> <HEM 105>: C2D C3D C1D CMD
> <HEM 105>: C3A C4A C2A CMA
> <HEM 105>: C3B C4B C2B CAB
> <HEM 105>: C3C C4C C2C CAC
> <HEM 105>: C3D C4D C2D CAD
> <HEM 105>: C4A NA C3A CHB
> <HEM 105>: C4B NB C3B CHC
> <HEM 105>: C4C NC C3C CHD
> <HEM 105>: C4D ND C3D CHA
> total 337 improper torsions applied
> 20 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved.
>
> Can someone please help me with these error messages? I would really
> appreciate it.
>
> Best,
> Karan Mehra
> Chemical Engineering
> University of Virginia 2012
>
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>
>
--
Nitu Bansal
M.S Pharm III Sem
Research Scholar
Department of Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Fri Dec 10 2010 - 05:00:03 PST
