Re: [AMBER] AMBER 11 sander segmentation fault

From: case <>
Date: Mon, 23 Apr 2012 21:24:18 -0400

On Mon, Apr 23, 2012, Shuyi Cao wrote:
> I am trying to run simulation on a 300 aa protein with two inhibitors in
> the binding site. I used antechamber to prepare the parameter and used
> tleap to prepare my file and tried to run the simulation. No error message
> is shown. When I tried to do the first minimization, the error message came
> out as " Segmentation fault". I attached my file in the attachment. Could
> anyone tell me how to solve this problem?

Is there any output from sander at all? Set maxcyc=5 and ntpr=1 to get
more detailed output.

Use the "checkoverlap" in ptraj to look for bad contacts in the initial

Try the minimization in pmemd: sometimes that will give more useful error


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Received on Mon Apr 23 2012 - 18:30:04 PDT
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