On Fri, Feb 15, 2013, Symon Gathiaka wrote:
>
> The challenge is when trying to minimize the protein with both the
> cofactor and the peptide substrate for 200 steps in solution, the
> calculation stops at the 10th step and i get the error: Segmentation
> fault (core dumped). I have tried to use more memory but that doesn't
> seem to be the problem.
A seg fault provides no information about what went wrong. If you haven't
done so, be sure to set ntpr=1 and examine the energy output carefully to see
if there is odd behavior (esp. atoms that are too close together). It's worth
using the "checkoverlap" command in ptraj to look for bad contacts in your
initial structure. Or, run for 9 steps (before the crash), and examine the
output coordinates visually and with checkoverlap. You are looking for
something that is different between the ternary complex and the binary ones.
...good luck....dac
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Received on Fri Feb 15 2013 - 12:00:03 PST
