Very helpful, thank you!
So, if I understand this correctly, checkoverlap (using the default of
0.95) should not produce any results. additionally, I need to double check
that there aren't any H's too close to the phosphates.
On Wed, Apr 24, 2013 at 2:20 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 14:00:02 PDT
