I am new to CG simulations. After going through the tutorials and available online materials, I have managed to run the simulations for a protein disorder region using Martini-v3. However, during the back mapping to the all-atom representation of the system, I faced the below-mentioned error:
GROMACS VERSION:
MPI: false
/home/satyajit/satyajit/mediator/alphafold/Backward-master/backward.py -f em2.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname W
Error reading charmm27 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading amber to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading charmm36 to martini mapping for REYP (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ser.charmm36.map).
Error reading charmm27 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading charmm36 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading slipids to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading amber to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading slipids to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading amber to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading slipids to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading amber to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading charmm to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading amber to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Residues defined for transformation from martini to charmm36:
dict_keys(['CYS', 'VAL', 'ASP', 'DOPS', 'TYR', 'TRP', 'DOPC', 'PRO', 'LEU', 'REYP', 'SER', 'GB3', 'Gb3', 'ALA', 'DPPC', 'ASN', 'POPG', 'CHOL', 'POPC', 'DOPE', 'POPS', 'THR', 'DOPG', 'DPPG', 'GLU', 'GLN', 'LYS', 'DMPC', 'HIS', 'GLY', 'TOG', 'ARG', 'PHE', 'ILE', 'MET', 'TOCL2', 'POPE'])
None
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2023.4 (-:
Hi Users,
I am new to CG simulations. After going through the tutorials and available online materials, I have managed to run the simulations for a protein disorder region using Martini-v3. However, during the back mapping to the all-atom representation of the system, I faced the below-mentioned error:
Now executing...
../Backward-master/initram.sh -f em2.gro -o em2_charmm.gro -to charmm36 -p topol.top -sol W
GROMACS VERSION: MPI: false /home/satyajit/satyajit/mediator/alphafold/Backward-master/backward.py -f em2.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname W Error reading charmm27 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map). Error reading charmm36 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map). Error reading slipids to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map). Error reading amber to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map). Error reading charmm36 to martini mapping for REYP (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ser.charmm36.map). Error reading charmm27 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map). Error reading charmm36 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map). Error reading slipids to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map). Error reading amber to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map). Error reading charmm27 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map). Error reading charmm36 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map). Error reading slipids to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map). Error reading amber to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map). Error reading charmm27 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map). Error reading charmm36 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map). Error reading slipids to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map). Error reading amber to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map). Error reading charmm to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map). Error reading charmm36 to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map). Error reading charmm27 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map). Error reading charmm36 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map). Error reading slipids to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map). Error reading amber to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map). Residues defined for transformation from martini to charmm36: dict_keys(['CYS', 'VAL', 'ASP', 'DOPS', 'TYR', 'TRP', 'DOPC', 'PRO', 'LEU', 'REYP', 'SER', 'GB3', 'Gb3', 'ALA', 'DPPC', 'ASN', 'POPG', 'CHOL', 'POPC', 'DOPE', 'POPS', 'THR', 'DOPG', 'DPPG', 'GLU', 'GLN', 'LYS', 'DMPC', 'HIS', 'GLY', 'TOG', 'ARG', 'PHE', 'ILE', 'MET', 'TOCL2', 'POPE']) None gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2 :-) GROMACS - gmx grompp, 2023.4 (-:
Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/satyajit/satyajit/mediator/alphafold/med1 Command line: gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
Setting the LD random seed to 2127810943
Generated 689 of the 356590 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'molecule_0'
Excluding 1 bonded neighbours molecule type 'W'
ERROR 1 [file backmapped.top, line 14]: No such moleculetype NA
Program: gmx grompp, version 2023.4 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2556)
Fatal error: There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
My command line input is: ../Backward-master/initram.sh -f em2.gro -o em2_charmm.gro -to charmm36 -p topol.top -sol W
Any help will be appreciated.
With regards, Satyajit Khatua