FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Fri Aug 13 2021 - 03:26:03 CDT

Dear all,

I faced a problem with running MD simulation of phenylalanine (PHE) amino
acid, which has an aromatic side chain, using a polarizable force field. I‌
used the following script (using psfgen 2.0) to create drude-compatible
.psf and .pdb files:
package require psfgen
topology drude_toppar_2019/toppar_drude_master_protein_2019g.str
segment AP1 {
pdb PHE2.pdb
first NTES
last CTES
auto angles dihedrals
}
coordpdb PHE2.pdb AP1
guesscoord
writepdb phe.pdb
writepsf phe.psf

Uploading the phe.psf (file link
<https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view?usp=sharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHBty_GmJQ$ >)
and
phe.pdb (file link
<https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view?usp=sharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHDY9pe8ug$ >)
files in vmd shows that there is a bond (a rendered image is available here
<https://urldefense.com/v3/__https://drive.google.com/file/d/1Xlqzhq5JEiIRUa5YYoG9V-l5fBwG_-Eq/view?usp=sharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHAKkL-4zA$ >)
between the lone pair located in the middle of aromatic ring (type LPA1)
and CG atom of PHE (type CD2R6A ) which is the Carbon atom located on the
ring and interfacing the ring and backbone. However when I run a short
minimization simulation initially I receive the following error mentioning
no bond parameter file is found. I looked into the topology file (file link
<https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view?usp=sharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHBbu4XVdQ$ >)
and couldn't find such a bond. I have to say that I followed the same
procedure with aspartic acid (ASP), which has no aromatic ring, and
everything was OK. It seems this problem arises when using aromatic rings.
I would really appreciate it if anyone could guide me.

Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 20 0 0
Info: PERIODIC CELL BASIS 2 0 20 0
Info: PERIODIC CELL BASIS 3 0 0 20
Info: PERIODIC CELL CENTER 62 36 101
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
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 310
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 phe_min-heat.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME phe_min-heat
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME phe_min-heat
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 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 2 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 20 20 20
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from
FFTW_NAMD_2.13_Linux-x86_64-netlrts.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.13_Linux-x86_64-netlrts.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
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 1628838807
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB phe.pdb
Info: STRUCTURE FILE phe.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
drude_toppar_2019/toppar_drude_master_protein_2019g.str
Info: PARAMETERS
drude_toppar_2019/toppar_drude_d_aminoacids_2019g.str
Info: PARAMETERS
drude_toppar_2019/toppar_drude_carbohydrate_2019a.str
Info: PARAMETERS
drude_toppar_2019/toppar_drude_nucleic_acid_2017c.str
Info: PARAMETERS drude_toppar_2019/toppar_drude_lipid_2017c.str
Info: PARAMETERS drude_toppar_2019/toppar_drude_model_2019g.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
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 453 BONDS
Info: 1097 ANGLES
Info: 3641 DIHEDRAL
Info: 121 IMPROPER
Info: 15 CROSSTERM
Info: 173 VDW
Info: 343 VDW_PAIRS
Info: 38 NBTHOLE_PAIRS
Warning: Reading PSF supporting DRUDE without enabling the Drude model in
the simulation config file
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS 40 23)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 (ATOMS
40 23)

[0] Stack Traceback:
  [0:0] [0x4f9dfd]
  [0:1] [0xdb1481]

Links:
image:
https://urldefense.com/v3/__https://drive.google.com/file/d/1Xlqzhq5JEiIRUa5YYoG9V-l5fBwG_-Eq/view?usp=sharing__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHAKkL-4zA$
psf file:
https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHBbtfmvhQ$
pdb file:
https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHDZMuhApQ$
topology file:
https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!pVzbXXdQrUYqAsmV6IDv3mcILfWkZo-v_L3rMHmwTe1-80_HSg2xAn23DHBv4ZwJtg$

All the best,
Zeynab

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