Hello,
I have been trying to do MD simulation on myoglobin in AMBER.
To do so, I used the parameter file of updated Gilmma heme parameter (
http://archive.ambermd.org/201012/att-0192/) and couldn't get success to
create the parameter files from them.
Could you please let me know how i can deal the protein with heme-co ???
I just tried with myoglobin contains heme+co and got error on reading it...
Its really appreciated if you could give some hints on this. Thanks a lot
for your time. Have a good day
Kind regards
Rajiv
On Mon, Mar 17, 2014 at 1:57 PM, Rajiv Gandhi <grajiv03.gmail.com> wrote:
> Hello,
>
> I have been trying to do MD simulation on myoglobin in AMBER.
>
> To do so, I used the parameter file of updated Gilmma heme parameter (
> http://archive.ambermd.org/201012/att-0192/) and couldn't get success to
> create the parameter files from them.
>
> Could you please let me know how i can deal the protein with heme-co ???
>
> I just tried with myoglobin contains heme+co and got following results.
>
> Its really appreciated if you could give some hints on this. Thanks a lot
> for your time. Have a good day
>
> *I only getting this error : *
>
> [bmdrc0.bravo raju]$ tleap
> -I: Adding /share/apps/amber12//dat/leap/prep to search path.
> -I: Adding /share/apps/amber12//dat/leap/lib to search path.
> -I: Adding /share/apps/amber12//dat/leap/parm to search path.
> -I: Adding /share/apps/amber12//dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: ./leaprc.ff99SB
> ----- Source of ./leaprc.ff99SB done
> Log file: ./leap.log
> Loading parameters: /share/apps/amber12//dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters: /share/apps/amber12//dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /share/apps/amber12//dat/leap/lib/all_nucleic94.lib
> Loading library: /share/apps/amber12//dat/leap/lib/all_amino94.lib
> Loading library: /share/apps/amber12//dat/leap/lib/all_aminoct94.lib
> Loading library: /share/apps/amber12//dat/leap/lib/all_aminont94.lib
> Loading library: /share/apps/amber12//dat/leap/lib/ions94.lib
> Loading library: /share/apps/amber12//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
> Unknown keyword:
> in parameter file. Perhaps a format error?
> Unknown keyword:
> in parameter file. Perhaps a format error?
> Unknown keyword:
> in parameter file. Perhaps a format error?
> Unknown keyword:
> in parameter file. Perhaps a format error?
> > 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
> > loadoff co.lib ( I created this to represent CO as diatomic mol in leap
> library )
> Loading library: ./co.lib
> > X=loadpdb check.pdb
> Loading PDB file: ./check.pdb
> Warning: name change in pdb file residue 1 ;
> this residue is split into HEM and CMO.
> 1 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
> Added missing heavy atom: .R<CGLY 153>.A<OXT 8>
> +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
> One sided connection. Residue: default_name missing connect0 atom.
> total atoms in file: 2541
> Leap added 5 missing atoms according to residue templates:
> 1 Heavy
> 4 H / lone pairs
> > check X
> Checking 'X'....
> WARNING: The unperturbed charge of the unit: 12.000000 is not zero.
> FATAL: Atom .R<CMO 155>.A<LO 2> does not have a type.
> FATAL: Atom .R<CMO 155>.A<LC 1> does not have a type.
> Warning: Close contact of 1.139998 angstroms between .R<HIP 24>.A<HE2 14>
> and .R<HIP 119>.A<HE2 14>
> Warning: Close contact of 0.994947 angstroms between .R<HIP 93>.A<HE2 14>
> and .R<HEM 154>.A<FE 1>
> Checking parameters for unit 'X'.
> Checking for bond parameters.
> Could not find bond parameter for: -
> Checking for angle parameters.
> There are missing parameters.
> check: Errors: 2 Warnings: 3
>
>
> *After mentioning the bond, i get more error as follows: *
>
> > bond X.93.NE2 X.154.FE
> > bond X.154.FE X.155.LC <http://x.155.lc/>
> > check X
> Checking 'X'....
> WARNING: The unperturbed charge of the unit: 12.000000 is not zero.
> FATAL: Atom .R<CMO 155>.A<LO 2> does not have a type.
> FATAL: Atom .R<CMO 155>.A<LC 1> does not have a type.
> Warning: Close contact of 1.139998 angstroms between .R<HIP 24>.A<HE2 14>
> and .R<HIP 119>.A<HE2 14>
> Warning: Close contact of 0.994947 angstroms between .R<HIP 93>.A<HE2 14>
> and .R<HEM 154>.A<FE 1>
> Checking parameters for unit 'X'.
> Checking for bond parameters.
> Could not find bond parameter for: NA - FE
> Could not find bond parameter for: FE -
> Could not find bond parameter for: -
> Checking for angle parameters.
> 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 -
> Could not find angle parameter: CR - NA - FE
> Could not find angle parameter: NO - FE -
> Could not find angle parameter: NP - FE -
> Could not find angle parameter: NO - FE -
> Could not find angle parameter: NP - FE -
> Could not find angle parameter: FE - -
> There are missing parameters.
> check: Errors: 2 Warnings: 3
>
> Kind regards
>
> Rajiv
>
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Received on Mon Mar 17 2014 - 00:00:02 PDT
