Re: [AMBER] MD stops due to the distortion of a molecule

From: David A Case <>
Date: Thu, 17 May 2018 08:11:48 -0400

On Thu, May 17, 2018, Sergey Samsonov wrote:

> ...when I simulate a protonated N-phosphate HO-PO2-NH-(sugar
> ring), the simulation goes well for certain time, which is always different
> and could vary from hundreds of picoseconds to tens of nanoseconds, but then
> it stops.

Check the LJ radius for the H in the protonated phosphate. If it has a
zero radius, that hydrogen can get too close to another atom (of
negative partial charge), leading to an arbitrarily large electrostatic
interaction. We've seen this problem with the H bonded to O in a
protonated phosphate, but I'd also check the H bonded to N, since this
is what is different between and N-phosphate and an O-phosphate. (On
the other hand, you report a lack for problems deprotonated

If either of these hydrogens have zero radii, try an experiment where
they have non-zero radii. In GAFF2, zero radii hydrogens have been
removed, and these parameters substituted:

    hn 0.6210 0.0100
    ho 0.3019 0.0047

This might be a good start to see if such a change has a effect on the
problem you report.

Of course, I'm just guessing here. But problems like you report have
been seen for protonated phosphates in other situations, so it's worth a

...good luck....dac

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Received on Thu May 17 2018 - 05:30:04 PDT
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