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Re: [lammps-users] converting pdb to lammps data file
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Re: [lammps-users] converting pdb to lammps data file

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 18 Sep 2017 07:19:52 -0400

On Mon, Sep 18, 2017 at 6:50 AM, R. Varsha <varsharani.0909@...24...> wrote:
> Hello Neda,
> Yes you can create lammps data file from your pdb via topotools. First you
> have to load that pdb file in vmd and then open tk console and give the
> following command -
> topo writelammpsdata <output filename> <atom-style>
> for e.g.
> topo writelammpsdata full

that is bad advice. this command will indeed create a data file, but
such a data file is _very likely_ bogus, *especially* when the input
is only a pdb file.

building a correct data file (or rather a force field specific
topology in general) for a molecular system, requires a lot more
effort. there is not a simple automatic "conversion" simply because
the pdb file is lacking a lot of the necessary information. in
particular a pdb file is lacking:
- explicit atom type information (note, that the atom names in a pdb
rarely coincide with the atom types, which are force field specific)
- explicit bond/angle/dihedral/improper information. VMD will use
heuristics to reconstruct bonds, but those may not be accurate and
anything beyond is not created, since those are not needed for
- partial charge information. most conventional force fields require
an assignment of an force field specific atom type *and* a partial
charge. those are usually stored in residue specific databases. for
charmm, these are .rtf files, while a force field like OPLS/AA has an
increment system.

for proteins (and selected lipids) where _the pdb file follows
*strictly* the published naming conventions_ tools exist (e.g. charmm
(the program), psfgen, xleap/tleap, pdb2gmx and more) to process the
pdb file, often in an interactive process and requiring a suitable
force field specific database.

topotools in combination with VMD scripting *can* be used for this,
but it requires a significant amount of thinking and custom scripting
as shown by the simple examples here:


> Regards
> Varsha
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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.