Hello,
for the above topic I can not seem to complete the final CHARMM-GUI starting step of minimization of my protein-membrane implant
(step6.0). The README Script was successfully generated within the generated Gromacs file containing the below files:
toppar
topol.top
step7_production.mdp
step6.6_equilibration.mdp
step6.5_equilibration.mdp
step6.4_equilibration.mdp
step6.2_equilibration.mdp
step6.3_equilibration.mdp
step6.0_minimization.mdp
step6.1_equilibration.mdp
step5_input.psf
step5_input.gro
step5_input.pdb
README
index.ndx
The indicated parallelization and minimization within the README file are pasted below respectively:
# running parallelized simulation, you should check if you are using appropriate command line.
# For MPI parallelizing, we recommand following command:
# mpirun -np $NUM_CPU gmx mdrun -ntomp 1
set init = step5_input
set rest_prefix = step5_input
set mini_prefix = step6.0_minimization
set equi_prefix = step6.%d_equilibration
set prod_prefix = step7_production
set prod_step = step7
# Minimization
# In the case that there is a problem during minimization using a single precision of GROMACS, please try to use
# a double precision of GROMACS only for the minimization step.
gmx grompp -f ${mini_prefix}.mdp -o ${mini_prefix}.tpr -c ${init}.gro -r ${rest_prefix}.gro -p topol.top -n index.ndx
gmx_d mdrun -v -deffnm ${mini_prefix}
I navigated to my Working Directory containing the above files and within my iTerm pasted the above Minimization Command
which resulted in the below several errors:
Error in user input:
Invalid command-line options
In command-line option -f
File '.mdp' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -c
File '.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -r
File '.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
My understanding is that I am supposed to just input what I did; please let me know the exact command and or parallelization I would need to input to successfully generate my model minimization? (I could not discovery anywhere a direct tutorial on this topic.). Thanks if you can help:)
