AMBER Archive (2008)

Subject: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program

From: Mohd Farid Ismail (farid_at_ou.edu)
Date: Wed Feb 06 2008 - 16:07:55 CST

Hello,

 

I want to make a box of a simple molecule. So what I did is create the
molecule in a program called WebView Pro, and save the pdb file. With this
file, I was able to create .prepin file using antechamber, and using the
prepin file I was able to create the topology and coordinate files using
tleap. (All this is done on a Red Hat machine, using Amber 8, on Intel
platform. I am not sure of the compiler version).

 

After I did this, I want to make copies of the molecule such that there are
100 of such molecule. I was told by a senior that Amber 5 has Edit, that
will create multiple copies of this molecule (create the coordinates and
charges in a pdb file). Is there a similar program that I can use in Amber
8 to do this?

 

Thank you.

-Mohd Farid Ismail-

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