From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Aug 03 2016 - 10:11:51 CDT
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> 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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