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

From: Amir Hossein Saeedi <asaeedi@...7272...>
Date: Mon, 4 Dec 2017 15:53:22 +0000

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?

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