Msi2namd to convert to pdb/psf

Hi everyone,

I am very new in the field of MD Simulations. I have started with a simulation of clay in water (Dynamics of carbohydrate strands in water and interactions with clay minerals: influence of pH, surface chemistry, and electrolytes - Nanoscale (RSC Publishing)). I am using the montmorillonite_CEC90 structure and given force field from supplementary material.

I don’t know how to convert .car/.mdf to .pdb/.psf and then convert the forcefield to gromacs.
I have tried the following command but it’s too many forcefield/automass options applied to one input file (don’t know how to fix this)
$ ./msi2namd.exe -f montmorillonite_CEC90_pH3.car montmorillonite_CEC90_pH3.mdf -res -inp -o montmorillonite_CEC90_pH3.pdb montmorillonite_CEC90_pH3.psf -ignore -nocenter -print 3

Can anyone help me how to solve this problem?

My apologies if it may sounds obvious solution to some people but I am new trying to use this conversion and I am really stuck.

Thank you in advance.

Nikolina

Sorry, but you are asking in the wrong place. There is no msi2namd.exe program in LAMMPS. So your question is off-topic.

Ah sorry.
Thank you anyways. Enjoy (: