Hi Karen,
I saw your post on the mailing list and I wondered if you managed to load the HEME parameters into tleap
many thanks
Fati
________________________________
From: Karan Mehra [mailto:kkm7r.virginia.edu]
Sent: Sat 11/12/2010 19:24
To: AMBER Mailing List
Subject: Re: [AMBER] HEME parameters
So I tried replacing CYS to CYM for the cysteine that is interacting with
HEME but I still get similar error messages.
On Sat, Dec 11, 2010 at 12:16 AM, Nitu Bansal <nitubansal1986.gmail.com>wrote:
> Hi
> check it out, if CYS is forming disulphide bond than replace with CYX
> otherwise the one in interaction with the HEME should be renamed as CYM.
>
> On Sat, Dec 11, 2010 at 3:07 AM, Karan Mehra <kkm7r.virginia.edu> wrote:
>
> > Hi Neetu,
> >
> > I don't think the CYS residues are involved in Cystein bonding. I still
> > changed them from CYS to CYX, but I still get similar error messages.
> Are
> > these error caused by the acetyl group in the beggining of the sequence?
> >
> > Thanks,
> >
> > On Fri, Dec 10, 2010 at 7:33 AM, Nitu Bansal <nitubansal1986.gmail.com
> > >wrote:
> >
> > > 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
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > >
> > >
> > > --
> > > Nitu Bansal
> > > M.S Pharm III Sem
> > > Research Scholar
> > > Department of Pharmacoinformatics
> > > S.A.S Nagar NIPER Mohali (Chandigarh)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Karan Mehra
> > Chemical Engineering
> > University of Virginia 2012
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Nitu Bansal
> M.S Pharm III Sem
> Research Scholar
> Department of Pharmacoinformatics
> S.A.S Nagar NIPER Mohali (Chandigarh)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Karan Mehra
Chemical Engineering
University of Virginia 2012
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Received on Wed Mar 02 2011 - 04:00:02 PST
