Preparing PDB file

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1

Are you able to run simulation without any errors ?

I do not know how charmm2lammps works. If it were me I would look up the charmm forcefield parameters, convert the relavant units/expression in to lammps expressions for (dihedrals…) and run my simulation, validate it.

As I said before I am not familiar with charmm but I have given you a general flow of how to build lammps data file.

People who are familiar with charmm forcefiled can give you suggestions.

Arun

2

For now yes,

thanks!

While I searched the web I found a software which
probably is interesting for other people too:
MDWiZ, cf. http://www.ncbi.nlm.nih.gov/pubmed/24434017
(They show an example with LAMMPS in their paper)

Best,
S.