AMBER Archive (2008)

Subject: AMBER: How to create *.top & *.crd file with hexagonal lattice

From: Chin, Keith B (keith.b.chin_at_jpl.nasa.gov)
Date: Sun Nov 16 2008 - 19:02:05 CST

Hi all,

I've manually created a pdb file that's read into xleap in order to create *.top & *.crd files for sander MD simulation on ICE. My lattice is NOT box, but a hex lattice with alpha = 90 degrees, beta = 90 degrees, and gamma = 120 degrees.

Here're my procedures to create the ice *.top and *.crd file from my pdb file in xleap:

 1. > ice = loadpdb ice.pdb
 2. > setbox ice vdw 1.0
 3. > saveamberparm ice fn.top fn.crd
 4. Then, I manually changed the last line in *.crd file from alpha = 90 degrees, beta = 90 degrees, and gamma = 90 degrees to with alpha = 90 degrees, beta = 90 degrees, and gamma = 120 degrees

However, upon this manual change in *.crd file, sander does not seem to like it and errors out when I try to run my MD sim. The only change is the gamma angle from 90 to 120.

My MD output error is:

FATAL: Could not read velocities from Ice_TIP4P_216_3.crd

Are there additional procedures/changes to *crd & *top files necessary to make this happen?

Appreciate any advice and thanks.

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

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