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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 4 Dec 2017 11:58:52 -0500



On Mon, Dec 4, 2017 at 10:53 AM, Amir Hossein Saeedi via lammps-users <lammps-users@lists.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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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.