On Wed, Apr 24, 2013, Jonathan Gough wrote:
>
> I didn't mention before, but will now (as I believe this is the REAL issue)
> There are phosphates on a few residues.
Check to see if you have hydrogens somewhere that are getting very close to
the phosphate oxygens. For example, stop the MD simulation before the ****
start to appear, and use the checkoverlap command to look for close contacts.
Many hydrogens in Amber force fields have zero van der Walls radius, and can
get too close to phosphate groups. Of course, this is just a guess...there
might be some other type of bad overlap that is leading to this behavior.
Finding out what is going on is the first step towards a fix.
...dac
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Received on Wed Apr 24 2013 - 11:30:03 PDT
