Hello,
I am trying to setup a QM/MM calculation with a ligand (substrate) docked into the protein. For MM, I am using amber.
I have generated a correct pdb file however, every time I run through prepare.nw, I get this error indicating something is wrong with my amber.par file:
Undetermined force field parameters
Parameters could not be found for atom type OX
Parameters could not be found for bond type OX -CX ( O1 - C2 )DHB 1700 22450 22451 22751 1 0
Parameters could not be found for bond type CX -CX ( C2 - C4 )DHB 1700 22451 22453 22753 1 0
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* 0: pre_check failed 9999
**********
0::Received an Error in Communication
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 9999.
I have generated a amber.par file shown below (the substrate only contains oxygens, carbons and hydrogens), but I cannot find any standardized amber.par files to compare it to and troubleshoot. Any suggestions/recommendations to fix this problem?
amber.par:
#
- This is the AMBER99 standard parameter file for NWChem 4.0
Electrostatic 1-4 scaling factor 0.833333
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
- NX 14.01000 7.11280E-01 1.82400E-01 1 1111111111
- Q 7 3.55640E-01 1.82400E-01
OX 16.00000 6.35968E-01 1.76830E-01 1 1111111111
Q 8 3.17984E-01 1.76830E-01
CX 12.01000 3.59824E-01 1.90800E-01 1 1111111111
Q 6 1.79912E-01 1.90800E-01
Angles
- NC -CQ -O 1.00000 1.00000
- CQ -NC -C 1.00000 1.00000
- NC -C -CB 1.00000 1.00000
- C -CB -NC 1.00000 1.00000
- CB -NC -CB 1.00000 1.00000
- NC -CB -CA 1.00000 1.00000
- CA -CB -N* 1.00000 1.00000
- CB -N* -CB 1.00000 1.00000
- C -NC -CB 1.00000 1.00000
- NC -C -NA 1.00000 1.00000
- OH -P -OH 1.00000 1.00000
Bonds
- CQ -O 1.00000 1.00000
Improper dihedrals
- NC -NC -CQ -O 0.00000 0.00000 2
- CT -CB -N* -CB 0.00000 0.00000 2
Atoms
Fe 24.30500 4.30952E-02 1.36000E-01 1 1111111111
26 2.15476E-02 1.36000E-01
Atom types
Fe 26 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
End
Thanks
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