From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Mar 12 2019 - 22:13:43 CDT
The problem was a missing negative sign on the epsilon value.
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Tuesday, March 12, 2019 8:41 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Didn't Find vdw parameter QMMM
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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:36 CST