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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 07:47:02 -0400

a) it is a bad habit to "hijack" a thread, i.e. continue with a
completely different question. so if you have a new question, post it
in a new e-mail with a suitable subject line
b) i have no time to debug other people's work, especially not data
files. if you can provide *convincing proof*, that a) you did
everything correctly and b) that a piece of software that i have
written does not function as documented, then i may look into that.
but there are many, many ways to shoot yourself in the foot, that you
will have to figure out what is wrong yourself.

axel.

On Mon, Sep 18, 2017 at 7:35 AM, R. Varsha <varsharani.0909@...24...> wrote:
> Dear Axel,
> When I was creating lammps data file via vmd topotools I had two inputs,
> first pdb and second one was psf file.
> And the lammps data file which I got...was not right. Too many errors were
> there. You can see here. I have attached my lammps data file.
> Anyways, Thanks for your good advice.
>
>
> On Mon, Sep 18, 2017 at 4:53 PM, R. Varsha <varsharani.0909@...24...>
> wrote:
>>
>> 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
>>> >
>>> >
>>> > ------------------------------------------------------------------------------
>>> > Check out the vibrant tech community on one of the world's most
>>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> > _______________________________________________
>>> > lammps-users mailing list
>>> > lammps-users@lists.sourceforge.net
>>> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.