[AMBER] How to build Amber topology and other files for inorganic crystalline material?

From: malay rana <malayrana81.gmail.com>
Date: Sun, 9 Jan 2011 11:06:52 +0100

    I am a new user to Amber. I wanted to build amber topology and
forcefield/parameter files for
a crystalline material whose coordinates for one unit cell is attached with
this mail. In the single unit
 cell, all the atoms are not connected or bonded, in other sense, they are
very scattered, however,
 when one constructs the multiple cells then can get the whole crystalline
material where all the atoms
 have bondings, otherwise, it is difficult to guess the structure from
single unit cell. My goal is to utilize
 these files prepared for single unit cell in periodic MD simulation e.g.,
NAMD or Amber itself. The
 crystalline structure contains tetrahedral Zn atoms connected to
methyl-imidazolate (mIm) groups
 i.e. mIm----Zn----mIm unit. I am really not finding anyway to handle this
situation. It would really
 be very helpful for me if you can suggest or way out something to advance

Wishing your kind help.
With best regards,


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Received on Sun Jan 09 2011 - 02:30:03 PST
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