Re: Fatal Error: vdw atom type CC3161

From: Allen, Caley R (caley.allen_at_chemistry.gatech.edu)
Date: Wed Aug 03 2016 - 13:46:17 CDT

Thank you for the reply.

I did not include this par file. I have done so, and resubmitted the simulation. I will let you know how it goes.

Thank you.

Cheers,

Caley

________________________________
From: Chitrak Gupta <chgupta_at_mix.wvu.edu>
Sent: Wednesday, August 3, 2016 11:11:51 AM
To: NAMD list; Allen, Caley R
Subject: Re: namd-l: Fatal Error: vdw atom type CC3161

Hi Caley,

Did you include the par_all36_carb.prm file? I think this is the file that contains the CC3161 atom.

For future, if you need to find out which file contains the said atom, navigate to the path where you have all your par files and type this linux command

grep par* -e CC3161

(replace the CC3161 by whatever atom you got the error for)

Hope this helps,
Chitrak.

On Wed, Aug 3, 2016 at 10:53 AM, Allen, Caley R <caley.allen_at_chemistry.gatech.edu<mailto:caley.allen_at_chemistry.gatech.edu>> wrote:

Greetings.

I am attempting to melt the tails of a bilayer system using CHARMM36. The bilayer is composed of SAPI and DOPC, and there is a protein with HEME and solvated with TIP3P water. I made sure to put the par files (par_all36_prot.prm and par_all36_lipid.prm) before the stream files (toppar_all36_lipid_inositol.str, toppar_water_ions_try.str and toppar_all36_prot_heme.str). However I am still getting the "Fatal error: didn't find vdw parameter for atom type CC3161". I copied in some of the log file below. I know this atom type is found in SAPI, specifically it is referring to C12 in the glucose head group.

Any help with solving this problem would be appreciated.

Cheers,

Caley

Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 115 0 0
Info: PERIODIC CELL BASIS 2 0 112 0
Info: PERIODIC CELL BASIS 3 0 0 218
Info: PERIODIC CELL CENTER 1.3657 -0.4518 55.5636
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME DOPC-PI-1AKK.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME DOPC-PI-1AKK.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME DOPC-PI-1AKK
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME DOPC-PI-1AKK.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: ENERGY OUTPUT STEPS 50
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 500
Info: PRESSURE OUTPUT STEPS 50
Info: FIXED ATOMS ACTIVE
Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 120 112 224
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 5
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1470225193
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ionized.pdb
Info: STRUCTURE FILE ionized.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all36_prot.prm
Info: PARAMETERS par_all36_lipid.prm
Info: PARAMETERS toppar_all36_lipid_inositol.str
Info: PARAMETERS toppar_water_ions_try.str
Info: PARAMETERS toppar_all36_prot_heme.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: SUMMARY OF PARAMETERS:
Info: 206 BONDS
Info: 535 ANGLES
Info: 907 DIHEDRAL
Info: 48 IMPROPER
Info: 6 CROSSTERM
Info: 106 VDW
Info: 2 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CC3161
[0] Stack Traceback:

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