VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Sun Aug 15 2021 - 22:55:51 CDT

If I recall correctly, there was an issue with bonds to lone pairs in NAMD
2.13. Have you tried the same simulation in 2.14?

On Fri, 13 Aug. 2021, 7:30 pm zeynab hosseini, <hosseinizeynab93_at_gmail.com>
wrote:

> 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!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqofV9zk9Eg$>) and
> phe.pdb (file link
> <https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view?usp=sharing__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqoc9AjLEJw$>)
> 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!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqocvmeWmeg$>)
> between the lone pair located in the middle of aromatic ring (type LPA1)
> and CG atom of PHE (type CD2R6A ) which is the Carbon atom located on the
> ring and interfacing the ring and backbone. However when I run a short
> minimization simulation initially I receive the following error mentioning
> no bond parameter file is found. I looked into the topology file (file
> link
> <https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view?usp=sharing__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqofmb0ZApg$>)
> 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!ua4F92N6ZEG2_rxQt-DwWS0jzuONXe_zchnXaLJBDF4YZuVqJ_7NJkBtIzXn_JSLwQ$
> <https://urldefense.com/v3/__https://drive.google.com/file/d/1Xlqzhq5JEiIRUa5YYoG9V-l5fBwG_-Eq/view?usp=sharing__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqocvmeWmeg$>
> psf file:
> https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!ua4F92N6ZEG2_rxQt-DwWS0jzuONXe_zchnXaLJBDF4YZuVqJ_7NJkBtIzVYzvqVeA$
> <https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqocBWFGUww$>
> pdb file:
> https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!ua4F92N6ZEG2_rxQt-DwWS0jzuONXe_zchnXaLJBDF4YZuVqJ_7NJkBtIzXztzCgeg$
> <https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqoeqEEL5cA$>
> topology file:
> https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!ua4F92N6ZEG2_rxQt-DwWS0jzuONXe_zchnXaLJBDF4YZuVqJ_7NJkBtIzXcr6V-vw$
> <https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqoehbKDyEQ$>
>
> All the best,
> Zeynab
>