On Aug 11, 2011, at 10:56 AM, case wrote:
> On Thu, Aug 11, 2011, Nyla Zaman wrote:
>>
>>
>> -------------------------------------------------------
>> Amber 10 SANDER 2008
>> -------------------------------------------------------
>>
>
> Do the sander test cases run correctly? If so, try to take one of those
> inputs (e.g. in $AMBERHOME/test/dhfr), convert it to your system, and slowly
> try to morph the inputs that work into yours.
>
> If the test cases don't run, then you need to re-examine how you installed
> Amber.
>
> ....dac
>
Another possibility is that two atoms are so close their VDW energy
calculation causes floating point overflow.
This is the symptom I ran into when trying to run minimizations with packmol-
created starting PDB files: the output above, then sander just hung without
any further output.
In this case, nothing was wrong with sander and nothing was wrong with the input
file. It was the starting structure that was at fault. To diagnose this, try
running a single step and see if it completes with high energies (VDW or, maybe,
electrostatics.)
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Thu Aug 11 2011 - 09:30:02 PDT
