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 Thu Nov 08 2012 - 06:00:02 PST
