Re: Re: Didn't Find vdw parameter QMMM

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Mar 13 2019 - 13:35:58 CDT

The response isn't to *crash* (i.e., segfault). You get a warning when
reading the file and a fatal error only if the type of atom with the
bad/unrecognized/unsupported parameter is actually present.

Jim

On Wed, 13 Mar 2019, Brian Radak wrote:

> 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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