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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: Neda Rafiee <ne.rafiee@...444...>
Date: Mon, 18 Sep 2017 16:04:51 +0430

Thanks a lot Axel,
In fact I followed the tutorial, I used the following command for all of my atoms, for example for P I used:

set selpl [atomselect top {name P}]
$selpl set type PL
$selpl set mass 30.9740
$selpl set charge 1.500

and then, I used :
topo retypebonds
topo numbondtypes
topo guessangles
topo numangletypes
topo guessdihedrals
topo numdihedraltypes
topo writelammpsdata twoDPPC.data full

Actually the number of atom types, bond types, and angle types are correct but there is a problem with the number of dihedral types. Actually, I have 58 dihedral types but in the created data files there is only 43. Can you help me with this?
And what is your opinion with using Moltemplate in lammps to produce a data file?
Thanks
Neda


 

On Mon, Sep 18, 2017 at 3:49 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.