Convert lammps data file to pdb

Dear Users,

I have read that there are several tools to convert lammps data files to pdb files however it is mentioned that the force field cannot be converted. Besides that in case the force field is implemented into the lammps scrip and the lammps data file contain only number of atoms ,bonds angles hi-lo of the simulation box ,Atoms Bonds Angles etc can be converted without any problem? and if so is there any suggestion of creating pdb files since the format is a little bit tricky?

Thanks
Jim

2012/1/17 Jim Jim <[email protected]>:

Dear Users,

I have read that there are several tools to convert lammps data files to pdb

where?

files however it is mentioned that the force field cannot be converted.

you cannot store into a file format any information that the file format
cannot handle. a pdb file has no records for storing force field information,
how should be able to store it. this would be like trying to play a dvd in a
cd player.

Besides that in case the force field is implemented into the lammps scrip
and the lammps data file contain only number of atoms ,bonds angles hi-lo of
the simulation box ,Atoms Bonds Angles etc can be converted without any

the pdb format also contains no records to store angles. there is an entry
for bonds, but those are reserved for "non-standard" bonds and non-standard
residues, i.e. stuff that is written out in HETATM records and not in ATOM
records.

problem? and if so is there any suggestion of creating pdb files since the
format is a little bit tricky?

i disagree on the PDB format being tricky. it is well documented
and all you need to is have a look at how fortran formatted output
is programmed, or rather understand the format descriptors.

the other problem is, that a pdb file *requires* information, that is
not present as such in data files. how would you retrieve or generate
that information? you cannot automatically generate something
from nothing (well, you could, but that would have no meaning).

that all being said, if you know how to map the information that
*is* provided in a data file to additional(!) information that you(!)
know about your(!) system, then you can write a script that would
augment the information from what the data file contains with
the additional, system specific data.

my tool of choice for this purpose is VMD, but you can also
use Pizza.py or write your own custom script/program to do
what you want to do.

axel.

There are some tools in the LAMMPS tools dir
that convert both topology and force field info from other MD
codes into a LAMMPS-compatible format. E.g.t eh ch2lmp tool
will use PDB files created by CHARMM and assign CHARMM ff
params to the bonds, angles, etc and write out LAMMPS
data files that have all the info.

Steve