Hello
I am working on small molecules, such as butane, C2H6S2 dimethyldisulfide,…
How can I convert pdb format into lammps data file.
Vmd only know amino acids residue.
Thank you
Hello
I am working on small molecules, such as butane, C2H6S2 dimethyldisulfide,…
How can I convert pdb format into lammps data file.
there is not simple conversion, since the .pdb file does not provide
all the information that is needed to write a suitable data files. it
doesn't provide anything about atom charges, bonds, angles, dihedrals,
impropers and there corresponding types. to get a suitable data file
you have to provide this information, either from a database or by
reconstructing it.
Vmd only know amino acids residue.
VMD doesn't know _anything_ it only stores, uses and visualized the
information you provide. there are a small number of features that
use heuristics, e.g. residue names, atom names to infer information from it,
but if you change those names, VMD is helpless, since it doesn't
really know anything.
that being said, VMD has tools to do the database lookup for
structure components via the psfgen plugin and it has tools to
reconstruct bonded interaction definitions from the topology in
the topotools plugin. but in both cases _you_ have to add the
missing information to the respective tools and write scripts to
assign the parameters (which is actually much better done in
an input file rather than in a data file).
the third option is to write your own tool to generate a data file.
many people have done this before.
cheers,
axel.
The tools/ch2lmp tool will do it if you have a CHARMM force
field file and assuming you want to run your model with
CHARMM params.
Steve