QM/MM prepare does not recognize ligand in protein

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4:15:36 PM PST - Mon, Nov 16th 2015
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
.
.
.
.
.
.

*   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:
#
  1. 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
  1. NX 14.01000 7.11280E-01 1.82400E-01 1 1111111111
  2. 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
  1. NC -CQ -O 1.00000 1.00000
  2. CQ -NC -C 1.00000 1.00000
  3. NC -C -CB 1.00000 1.00000
  4. C -CB -NC 1.00000 1.00000
  5. CB -NC -CB 1.00000 1.00000
  6. NC -CB -CA 1.00000 1.00000
  7. CA -CB -N* 1.00000 1.00000
  8. CB -N* -CB 1.00000 1.00000
  9. C -NC -CB 1.00000 1.00000
  10. NC -C -NA 1.00000 1.00000
  11. OH -P -OH 1.00000 1.00000

Bonds
  1. CQ -O 1.00000 1.00000


Improper dihedrals
  1. NC -NC -CQ -O 0.00000 0.00000 2
  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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