Re: Re: Didn't Find vdw parameter QMMM

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Mar 13 2019 - 10:59:15 CDT

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> 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 <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*
>
>
>

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