[lammps-users] help regarding converting from pdb to lammps data file

LAMMPS LAMMPS Mailing List Mirror
1

dear lammps users,

suppose the bonds in pdb is defined as below
CONECT 37 34 38 39 56

how do we convert this to the lammps data file format???

thanking you
vishnu

2

dear vishnu,

dear lammps users,

suppose the bonds in pdb is defined as below
CONECT 37 34 38 39 56

how do we convert this to the lammps data file format???

you have to be a bit more specific about what is in the .pdb
file. how many atom types do you have in there? .pdb only has
the names field.

technically a conversion is possible using the latest VMD beta version.

you would type (on the VMD console window):

mol new <pdb filename> filebonds 1
package require topotools
topo writelammpsdata <data filename> <atom style>

and e-voila. but this way you would not have angle,
dihedral definitions etc.

cheers,
   axel.

3

The tools/ch2lmp/lammps2pdb.pl script does this. Also the
Pizza.py tools add-on package for LAMMPS (see link on LAMMPS
www page) can do this.

Steve