Dear all,
I am dealing with simulation of the horse Cyt c, which contains an HEME
group bound to the an HIS and MET. and I am using the HEME parameters from
the Cheatham et al.
https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21922
However, since this latter only accounts for the unbound HEME, I end up
with leap asking me
for the missing parameters that I do not have.
So, I wonder whether there is exist a way to include the parameters of the
HEME bound to the HIS and MET,, without though running any QM calculation
to get those values. If so, how can I make Leap read them ? Thanks in
advance for any tip.
Here is the leap script and its output when I run it.
*INPUT : *
source leaprc.protein.ff14SB
source leaprc.gaff
loadamberparams heme.frcmod # From CHeatham et. al
HEM = loadmol2 heme.mol2 # From CHeatham et. al
addAtomTypes {{ "fe" "Fe" "sp3" }}
hrc =loadpdb 1hrc_H.pdb # reduced 1hrc.pdb
saveamberparm hrc hrc.prmtop hrc.rst7
quit
*OUTPUT:*
I: Adding /home/emanuele/amber16/dat/leap/prep to search path.
-I: Adding /home/emanuele/amber16/dat/leap/lib to search path.
-I: Adding /home/emanuele/amber16/dat/leap/parm to search path.
-I: Adding /home/emanuele/amber16/dat/leap/cmd to search path.
-f: Source leap.src.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leap.src
----- Source: /home/emanuele/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /home/emanuele/amber16/dat/leap/cmd/leaprc.protein.ff14SB
done
Log file: ./leap.log
Loading parameters: /home/emanuele/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/emanuele/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/emanuele/amber16/dat/leap/lib/amino12.lib
Loading library: /home/emanuele/amber16/dat/leap/lib/aminoct12.lib
Loading library: /home/emanuele/amber16/dat/leap/lib/aminont12.lib
Could not open file leaprc.ff99SBildn: not found
----- Source: /home/emanuele/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /home/emanuele/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/emanuele/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Loading parameters: ./heme.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)
Loading parameters: ./giammona.frcmod
Modified force field files must contain both a MASS and NONB entry, or
neither
Could not load parameter set.
-- no parameters loadedLoading Mol2 file: ./heme.mol2
Reading MOLECULE named HEM-IC6
Loading PDB file: ./1hrc_H.pdb
+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: 1741
Leap added 8 missing atoms according to residue templates:
8 H / lone pairs
Checking Unit.
ERROR: The unperturbed charge of the unit: 6.402400 is not integral.
WARNING: The unperturbed charge of the unit: 6.402400 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - cc
Could not find bond parameter for: SH - cd
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 - cc
Could not find angle parameter: SH - cc - cd
Could not find angle parameter: SH - cc - ha
Could not find angle parameter: SH - cc - cd
Could not find angle parameter: 2C - SH - cc
Could not find angle parameter: HS - SH - cd
Could not find angle parameter: SH - cd - cc
Could not find angle parameter: SH - cd - ha
Could not find angle parameter: SH - cd - cc
Could not find angle parameter: 2C - SH - cd
Could not find angle parameter: CW - NA - fe
Could not find angle parameter: H - NA - fe
Could not find angle parameter: NA - fe - nc
Could not find angle parameter: NA - fe - nd
Could not find angle parameter: NA - fe - nc
Could not find angle parameter: NA - fe - nd
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 - nc
Could not find angle parameter: S - fe - nd
Could not find angle parameter: S - fe - nc
Could not find angle parameter: S - fe - nd
Could not find angle parameter: 2C - S - fe
Building proper torsion parameters.
** No torsion terms for HS-SH-cc-cd
** No torsion terms for HS-SH-cc-ha
** No torsion terms for HS-SH-cc-cd
** No torsion terms for 2C-SH-cc-cd
** No torsion terms for 2C-SH-cc-ha
** No torsion terms for 2C-SH-cc-cd
** No torsion terms for HS-SH-cd-cc
** No torsion terms for HS-SH-cd-ha
** No torsion terms for HS-SH-cd-cc
** No torsion terms for 2C-SH-cd-cc
** No torsion terms for 2C-SH-cd-ha
** No torsion terms for 2C-SH-cd-cc
** No torsion terms for CW-NA-fe-nc
** No torsion terms for CW-NA-fe-nd
** No torsion terms for CW-NA-fe-nc
** No torsion terms for CW-NA-fe-nd
** No torsion terms for CW-NA-fe-S
** No torsion terms for H-NA-fe-nc
** No torsion terms for H-NA-fe-nd
** No torsion terms for H-NA-fe-nc
** No torsion terms for H-NA-fe-nd
** No torsion terms for H-NA-fe-S
** No torsion terms for NA-fe-nc-cc
** No torsion terms for NA-fe-nc-cc
** No torsion terms for NA-fe-nd-cd
** No torsion terms for NA-fe-nd-cd
** No torsion terms for NA-fe-nc-cc
** No torsion terms for NA-fe-nc-cc
** No torsion terms for NA-fe-nd-cd
** No torsion terms for NA-fe-nd-cd
** No torsion terms for NA-fe-S-2C
** No torsion terms for NA-fe-S-CT
** No torsion terms for CR-NA-fe-nc
** No torsion terms for CR-NA-fe-nd
** No torsion terms for CR-NA-fe-nc
** No torsion terms for CR-NA-fe-nd
** No torsion terms for CR-NA-fe-S
** No torsion terms for CT-S-fe-nc
** No torsion terms for CT-S-fe-nd
** No torsion terms for CT-S-fe-nc
** No torsion terms for CT-S-fe-nd
** No torsion terms for S-fe-nc-cc
** No torsion terms for S-fe-nc-cc
** No torsion terms for S-fe-nd-cd
** No torsion terms for S-fe-nd-cd
** No torsion terms for S-fe-nc-cc
** No torsion terms for S-fe-nc-cc
** No torsion terms for S-fe-nd-cd
** No torsion terms for S-fe-nd-cd
** No torsion terms for 2C-S-fe-nc
** No torsion terms for 2C-S-fe-nd
** No torsion terms for 2C-S-fe-nc
** No torsion terms for 2C-S-fe-nd
Building improper torsion parameters.
total 316 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Quit
Cheers,
Manuele
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Mon Nov 18 2019 - 08:00:02 PST
