Re: [AMBER] Explicit water molecules in OPC vs TIP3P

From: David A Case <>
Date: Thu, 14 Oct 2021 08:58:38 -0400

On Thu, Oct 14, 2021, Lennart Gundelach wrote:
>The problem seems to be that can’t handle the 4-point water

This should get fixed. I've opened an issue on our gitlab site so at least
the information won't get lost.

>If I strip out all the 4th “atom” form the OPC model, leaving only
>the two Hydrogens and the Oxygen, from the input files (obviously this is
>a terrible idea), runs without problems, just give pretty silly

Can you say exactly what you did to strip out the OPC extra point?
Logically, the extra point information is not needed, since its position is
computed on the fly from the coordinates of the oxygen and hydrogens. But
the code probably expects it to be there.

Also, did you manually strip the waters (except the ones you want to keep)
from the trajectories, or did you rely on the MMPBSA code to do that for
you? (Sorry if this doesn't make sense: I don't use this code myself. But
if you just have prmtop and trajectory files that include a few OPC waters,
I don't see why the MMPBSA code should care whether they are three-point or
four-point waters; the prmtop files know such details.)

Of course, if you can come up with a small test case that illustrates the
problem, that would be a great help.


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Received on Thu Oct 14 2021 - 06:00:02 PDT
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