Didn't Find vdw parameter QMMM

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 12 2019 - 21:41:31 CDT

I keep getting this error even though the parameters are provided:

Info: PARAMETERS Cu_qwikmd.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Warning: Ignoring VDW parameter with negative epsilon:
CU 0.0 0.00148497 1.218000 ! Cu II
Info: SUMMARY OF PARAMETERS:
Info: 937 BONDS
Info: 2734 ANGLES
Info: 6671 DIHEDRAL
Info: 203 IMPROPER
Info: 6 CROSSTERM
Info: 358 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CU

Here is my code:

# Force Field Parameters

paratypecharmm on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
parameters Cu_qwikmd.str
exclude scaled1-4
1-4scaling 1.0
rigidbonds none

And the Cu_qwikmd.str file:

* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

MASS 84 CU 63.546

RESI COP 2.000
ATOM CU CU 2.00

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!

CU 0.0 0.00148497 1.218000 ! Cu II

END

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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