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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: "R. Varsha" <varsharani.0909@...24...>
Date: Mon, 18 Sep 2017 16:53:24 +0530

Thanks Axel.!

Neda, follow Axel.


Regards,
Varsha

On Mon, Sep 18, 2017 at 4:49 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
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 lmp.data 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
visualization
- 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:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2

axel.


>
>
> Regards
> Varsha
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.