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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 07:55:45 -0400

On Mon, Sep 18, 2017 at 7:34 AM, Neda Rafiee <ne.rafiee@...444...> wrote:
> 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 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?

no. i have no time to do your work. topotools is not designed to be a
simple automated topology builder tool (one could program one on top
of it, but i don't have the interest or the time), but a tool that
simplifies topology manipulations, that other automated tools cannot
do easily. thus, as a "close to the metal" tool, it is very much a
tool for people that know what they are doing or those that spend the
time to carefully test and understand each step of what they are

mind you, the topotools tutorial is only an example and only for a
force field that doesn't require a residue template database to look
up topology, atom type and charge data.

> And what is your opinion with using Moltemplate in lammps to produce a data
> file?

topotools and moltemplate are different tools with different goals. i
have never used moltemplate.


> 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 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:
>> axel.
>> >
>> >
>> > 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.

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