Re: [AMBER] Distorted and Failed Phosphate Simulations

From: David A Case <>
Date: Thu, 19 Nov 2015 08:26:20 -0500

On Thu, Nov 19, 2015, Sigurd Friis Truelsen wrote:
> I have problems running regular MD simulations with inorganic
> phosphate HPO4(2-), H3PO4(-) and H3PO4 .

A "typical" problem with protonated phosphates is that a hydrogen can be
attracted to a neighboring oxygen on the same phosphate, and there is no
Lennard-Jones term on the hydrogen to prevent it from collapsing onto the
oxygen. I'm not sure whether this is the cause of your problems or not, but
you should monitor MD or minimzation carefully to look for such interactions.

Although it is a kludge, it generally works to increase the O--P--O and
P--O--H angle force constants to enforce a conventional geometry about the
phorphorus and prevent such intramolecular H--O interactions from ocurring.
Take a look at the frcmod.phosaa10 file (in $AMBEHROME/dat/leap/parm), which
has parameters we use for phosphorylated amino acids, along with comments
about how the angle parameters were determined. A similar strategy is likely
to work for phosphate itself.


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Received on Thu Nov 19 2015 - 05:30:06 PST
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