AMBER Archive (2008)

Subject: AMBER: Sander *.top and *.crd file from PDB file

From: Chin, Keith B (
Date: Fri Nov 14 2008 - 13:43:41 CST


I'm using Amber9 in an attempt to simulate bulk and surface ice.

I created a pdb file of ice lattice containing 216 TIP4P water molecules which successfully loads in xleap. From xleap, I was able to generate *.top and *.crd files for min and md simulations using sander.

Problem: During sander min run, the run just stays active BUT produced no results. My min.out file contains only the Amber header after I terminated the run using Cntl + C unix command.

I interpret this as an *.top issue. I'm not sure if I set my periodic boundary conditions correctly for 216 water molecule in ice lattice. My lattice dimensions for this ice lattice are: x= 13.548A, y= 27.096A, y= 22.062, alpha = 90, beta=90, and gamma = 120.

Does xleap automatically recognize these dimensions from my pdb file for do I have to set it manually as well? If so, do I use xleap or ptraj for this process?

Any advise would be greatly appreciated.

Keith Chin
Electrochemical Technologies Group
Office: (818) 354 - 4051

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