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Re: [lammps-users] Lammps data file
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Re: [lammps-users] Lammps data file


From: Myatnoe Suukyi <myatnoesuukyi@...444...>
Date: Thu, 7 Dec 2017 14:19:52 +0000

Thanks a lot. this info is very helpful for me as well.

On Wed, Dec 6, 2017 at 11:14 PM, Andrew Jewett <jewett@...1937...> wrote:
On Tue, Dec 5, 2017 at 6:38 AM, Myatnoe Suukyi via lammps-users
<lammps-users@...429...96...sourceforge.net> wrote:
> Hi Amir and lammps users
> This website has PDB files for hydrocarbon.
> https://www.nyu.edu/pages/mathmol/library/hydrocarbons/
> best regards,
> suu

> On Mon, Dec 4, 2017 at 4:58 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>> however, these atom names/element are usually different from atom types in
>> force fields, and how atom types for force fields are assigned is specific
>> to the individual force field or parameter set. there is no general rule,
>> since different force fields can have very different procedures. many
>> established force fields have their own tools to do atom typing, however,
>> they will only work for known any recognized molecules or fragments.

The atom type names contained in PDB files are often too vague to
determine force field parameters (and some PDB files don't follow the
popular naming conventions).

As Axel said, popular force fields (like OPLSAA, CHARMM, COMPASS,
GROMOS, AMBER, PCFF,...) have different ways of assigning names to the
same atom types.  For example, the COMPASS force field (the
published_version) has 11 different types of carbon atoms, each with
different type names, and appearing in different chemical groups.
AMBER/GAFF2 has 19 carbon atom types, OPLSAA has a varying number of
carbon atom types (depending upon how you want to assign partial
charge).  For each of these force fields, each of these carbon atom
types has a different name, and that name usually does not match the
atom name in the PDB file.  (The same is true for oxygen, sulfer,
hydrogen, ...)

Molecule building programs lookup the field information using these
force-field-specific atom names.  (Not the names in the PDB file.)
Fortunately, some of these programs (such as AmberTools, VMD?,
gromacs?, and possibly MedeA and MaterialsStudio, and EMC) might be
able too infer these specific atom types directly from the information
in the PDB file (a process called "atom typing") and then lookup force
field parameters.  (I'm curious to know which tools do this well.)
Otherwise you have to specify these force-field-specific atom names
manually (or specify the actual force field parameters themselves
manually).  But everything depends on which force field you want to
use.

In any case, the first step is to choose your force field appropriate
for the types of molecules you want to simulate.  Then pick the tool
for building your simulation input files (data files, input scripts)
which is most appropriate for that force field, and preferably is
actively maintained.  More programs are listed here (although some of
them only generate input geometry):

http://lammps.sandia.gov/prepost.html
https://sourceforge.net/projects/moleculardynami/
(disclaimer: I wrote one of these tools)
(Also see "ch2lmp", "amber2lmp", and "msi2lmp" in the lammps' "tools"
subdirectory.  Some of these tools have unpatched bugs or are
unsupported.  If you use "moltemplate", download the latest version
from moltemplate.org.)

I don't know if this helped.

-Andrew


> On Mon, Dec 4, 2017 at 4:58 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>> On Mon, Dec 4, 2017 at 10:53 AM, Amir Hossein Saeedi via lammps-users
>> <lammps-users@...396...sourceforge.net> wrote:
>>>
>>> Dear All
>>>
>>> I'm going to build a data file, containing bonds/angles/ dihedrals, from
>>> a pdb file using VMD topotool.
>>>
>>>
>>> However, I think vmd guesses bonds according to atom types and
>>> coordinates. Is there any naming convention for atom naming in pdb? If yes,
>>> could anybody introduce an appropriate link. Also, is there any preprocessor
>>> for automatically generating such standard names for a given molecule?
>>
>>
>> VMD guesses bonds based on elements. a complete and standard conforming
>> PDB format file will provide those. if those are not present, VMD will guess
>> elements based on the atom "names", which are assigned based on
>> geometry/topology. the PDB format and its naming conventions is well
>> documented (and declared obsolete, BTW).
>>
>> however, these atom names/element are usually different from atom types in
>> force fields, and how atom types for force fields are assigned is specific
>> to the individual force field or parameter set. there is no general rule,
>> since different force fields can have very different procedures. many
>> established force fields have their own tools to do atom typing, however,
>> they will only work for known any recognized molecules or fragments.
>>
>> any kind of automated tools usually introduce errors, either through lack
>> of specificity or mismatched fragments or missing specific parameters. you
>> will have to work this out on your own and follow the rules given for the
>> force field or parameter set you want to use. everybody has. there ain't no
>> escape from the blues.
>>
>> axel.
>>
>>>
>>>
>>> I made some trials in Avogadro and Arguslan. But, they are inappropriate.
>>>
>>>
>>>
>>> With Kind Regards
>>>
>>> Saeedi Dehaghani Amir Hossein
>>> Assistant Professor
>>> Department of Petroleum Engineering
>>> Faculty of Chemical Engineering
>>> Tarbiat Modares University
>>> Address: Tarbiat Modares University, Jalal Ale Ahmad Highway, Gisha
>>> Bridge, Tehran, Iran
>>> Mob: +98-9122892230
>>> Tel: +98 21 82883350
>>> Fax: +98 21 82883350
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>> _______________________________________________
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>>> lammps-users@...396...sourceforge.net
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>>>
>>
>>
>>
>> --
>> 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.
>>
>>
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>
>
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