[lammps-users] PDB <--> LAMMPS small peptide input

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1

Hi all,

I need to do a series of simulation replicates with various small
peptides and peptide clusters. I have structures now only in PDB
format. As I understand there is no conversion tool to a LAMMPS input
file directly from PDB. If so, what other options exist? How have
people typically approached this conversion in the past, other than by
painstaking manual rewriting of the structures.

Thanks!

2

Hi all,

I need to do a series of simulation replicates with various small
peptides and peptide clusters. I have structures now only in PDB
format. As I understand there is no conversion tool to a LAMMPS input
file directly from PDB. If so, what other options exist? How have
people typically approached this conversion in the past, other than by
painstaking manual rewriting of the structures.

i've been using psfgen (bundled with VMD) to generate a
.psf file and then use the chm2lmp converter to generate
lammps input. it is important to note that chm2lmp does
not support the CMAP corrections...

cheers,
   axel.

3

The README in tools/ch2lmp describes how to do
this conversion.

Steve