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

From: Sergey Samsonov <>
Date: Fri, 18 May 2018 08:13:43 +0200

Dear David,

Thank you very much for your help. Indeed, the problem was that HO was
used from parm99:

HO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657

So, changing it to Ho from GLYCAM06:

Ho          0.2000  0.0300             M.B. Tessier 2011

solved everything.

Probably, in O-sulfate, the conformational accessibility of the
orientations of HO, which lead to the unphysically high eletrostatic
interactions, is different from N-sulfate. Therefore, such an effect is
not observed for O-sulfates.

Thanks a lot and cheers,


On 17.05.2018 14:11, David A Case wrote:
> 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
> N-phosphates.)
> 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
> look.
> ...good luck....dac
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Sergey Samsonov, PhD
Project Leader at Laboratory of Molecular Modeling,
Department of Theoretical Chemistry,
Faculty of Chemistry,
University of Gdansk
ul. Wita Stwosza 63
80-308 Gdańsk, Poland
phone: +48 58 523 5166
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Received on Thu May 17 2018 - 23:30:03 PDT
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