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
structure.
Try the minimization in pmemd: sometimes that will give more useful error
messages.
.....dac
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Received on Mon Apr 23 2012 - 18:30:04 PDT
