AMBER Archive (2008)

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

From: Gustavo Seabra (
Date: Fri Nov 14 2008 - 14:30:21 CST

On Fri, Nov 14, 2008 at 2:43 PM, Chin, Keith B wrote:
> Hi,
> 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.

You will need to give us more information here.
1. Does sander pass all the test cases?
2. What actually is in the output file?
3. What actually is your input file?

What specifically makes you think it is a prmtop or box size issue?

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
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