Dear list,
maybe I should ask my question differently. Can I ignore this section and still get a reasonable MD simulation?
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- 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: *-NA-FE-*
+--- 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: *-ND-FE-*
+--- 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: *-NC-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
If yes could you explain me why? If not is it okay to add by hand { "fe" "Fe" "sp3" } as definition? Or does it sound fishy?
Thank you very much,
Max
On 2012-11-08, at 8:35 AM, Maximilian Ebert <m.ebert.umontreal.ca> wrote:
> Dear list,
>
> I previously started a thread here and I was able to solve most of my question. The last remaining issue I have is regarding the heme iron in my preparation. The coordinate and parameter file created by tleap now are already accepted by NAMD and the simulation runs without crashing. However, I have some concerns about how I treated the heme iron. I used the heme and heme-cysteine frcmod / mol2 files from Dr. Cheatham's paper from 2011. The output I show here is if I don't add the following line to leaprc.ff99SBildn: { "fe" "Fe" "sp3" }. If I add the atom type like this no error is produced. Can I just do that? Or should I ignore the warning about the hybridization? Would it make a difference for the MD simulation?
>
> Thank you very much,
>
> Max
>
> ../Downloads/amber12/bin/tleap -f leaprc.ff99SBildn -f leaprc.gaff
> -I: Adding /Users/doom4/Downloads/amber12//dat/leap/prep to search path.
> -I: Adding /Users/doom4/Downloads/amber12//dat/leap/lib to search path.
> -I: Adding /Users/doom4/Downloads/amber12//dat/leap/parm to search path.
> -I: Adding /Users/doom4/Downloads/amber12//dat/leap/cmd to search path.
> -f: Source leaprc.ff99SBildn.
> -f: Source leaprc.gaff.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: /Users/doom4/Downloads/amber12//dat/leap/cmd/leaprc.ff99SBildn
> Log file: ./leap.log
> Loading parameters: /Users/doom4/Downloads/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: /Users/doom4/Downloads/amber12//dat/leap/parm/frcmod.ff99SBildn
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling) + ILDN corrections
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/all_nucleic94.lib
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/all_amino94ildn.lib
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/all_aminoct94ildn.lib
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/all_aminont94ildn.lib
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/ions94.lib
> Loading library: /Users/doom4/Downloads/amber12//dat/leap/lib/solvents.lib
> Sourcing: /Users/doom4/Downloads/amber12//dat/leap/cmd/leaprc.gaff
> Log file: ./leap.log
> Loading parameters: /Users/doom4/Downloads/amber12//dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
>> loadamberparams hem.frcmod
> Loading parameters: ./hem.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Ferric-high-spin.frcmod- Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem (2011)
>> CYP = loadmol2 cys.mol2
> Loading Mol2 file: ./cys.mol2
> Reading MOLECULE named CYP-IC6
>> HEM = loadmol2 hem.mol2
> Loading Mol2 file: ./hem.mol2
> Reading MOLECULE named HEM-IC6
>> pdb = loadpdb cypmoeheditv2.pdb
> Loading PDB file: ./cypmoeheditv2.pdb
> One sided connection. Residue: CYP-IC6 missing connect0 atom.
> One sided connection. Residue: default_name missing connect1 atom.
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NB-FE-*
> +--- 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: *-NA-FE-*
> +--- 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: *-ND-FE-*
> +--- 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: *-NC-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> total atoms in file: 7383
>> saveamberparm pdb cyth.prmtop cyth.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1448 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CGLY 1
> CYP 1
> HEM 1
> NTHR 1
> )
> (no restraints)
>
>
>
>
>
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Received on Fri Nov 09 2012 - 12:00:02 PST
