VMD-L Mailing List

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Mon Aug 16 2021 - 01:19:35 CDT

Hi Michael,

Thank you for your reply. As you said I tried both versions NAMD 2.14 and
Nightly build, but still receiving the same error. Do you have any other
ideas? I really need to get this work and I don't know what to do.. It only
works when removing the lone-pair bond, but the resulting output is a
messed-up structure.

I also noticed a warning before the FATAL ERROR as follows. Isn't it
strange that it reads PSF without enabling the Drude model?

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)

All the best,
Zeynab

On Sun, Aug 15, 2021 at 11:56 PM Michael Robinson <
michael.robinson1_at_monash.edu> wrote:

> 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!roqDppNsBiWq3SIqolxYa6xd8gaGJCBvtJMNB1Hqk2OIgD8_TPMkUoHdKfhiUxnHdw$
>> <https://urldefense.com/v3/__https://drive.google.com/file/d/1Xlqzhq5JEiIRUa5YYoG9V-l5fBwG_-Eq/view?usp=sharing__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqocvmeWmeg$>
>> psf file:
>> https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!roqDppNsBiWq3SIqolxYa6xd8gaGJCBvtJMNB1Hqk2OIgD8_TPMkUoHdKfiu5FUxVw$
>> <https://urldefense.com/v3/__https://drive.google.com/file/d/12CpZSCXY0183F7c7z0Xrvv83vGZv4Enl/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqocBWFGUww$>
>> pdb file:
>> https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!roqDppNsBiWq3SIqolxYa6xd8gaGJCBvtJMNB1Hqk2OIgD8_TPMkUoHdKfi33OMXkA$
>> <https://urldefense.com/v3/__https://drive.google.com/file/d/1cFDOwGXfbfizcKT8kYYux3aMd0PHDRL2/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqoeqEEL5cA$>
>> topology file:
>> https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!roqDppNsBiWq3SIqolxYa6xd8gaGJCBvtJMNB1Hqk2OIgD8_TPMkUoHdKfhSpX-wEg$
>> <https://urldefense.com/v3/__https://drive.google.com/file/d/1rEIvG-Uv0ZBmAr8Lc2FQmO13wCmx65pp/view__;!!DZ3fjg!u35JmHz7JRoFCe6g9D6HoP652-fphfBUE6BlLDdpOCm_GfsElIkFozyAqoehbKDyEQ$>
>>
>> All the best,
>> Zeynab
>>
>