Re: Re: Didn't Find vdw parameter QMMM

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Mar 14 2019 - 01:48:03 CDT

Brian, I used a regular .prm file, and still had the problem. Adding the negative sign in front of the epsilon value fixed it again.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Brian Radak <brian.radak_at_gmail.com>
Sent: Wednesday, March 13, 2019 9:59 AM
To: namd-l; McGuire, Kelly
Subject: Re: namd-l: Re: Didn't Find vdw parameter QMMM

That's odd. My recollection was that the negative sign was an old system for flagging different mixing rules (negative = geometric, positive = arithmetic). While it's true that NAMD never supported this syntax (there's a global keyword for it instead), I'd be surprised if the response was to crash.

Could you also try with just plain .prm syntax without all of the .str contents?

BKR

On Tue, Mar 12, 2019 at 11:15 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
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<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>>
Sent: Tuesday, March 12, 2019 8:41 PM
To: namd-l_at_ks.uiuc.edu<mailto: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 : Sun Dec 08 2019 - 23:20:33 CST