Hi,
The source of her problem was probably missing TER cards;
make sure that the HEM residue is sandwiched between TER cards
or else LEaP will attempt to form bonds to the HEM from the
surrounding residues possibly resulting in missing parameters.
scott
On Wed, Mar 02, 2011 at 11:53:54AM -0000, CHAMI F. wrote:
>
> I saw your post on the mailing list and I wondered if you managed to load the HEME parameters into tleap
>
> 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:
>
> > 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.
> > > > >
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Received on Thu Mar 03 2011 - 19:30:03 PST
