Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch

From: Hannes Loeffler <>
Date: Wed, 13 Jan 2016 15:03:10 +0000

On Wed, 13 Jan 2016 20:09:13 +0530
tarak karmakar <> wrote:

> Could you please comment on the issue that I am facing in my
> simulation?

The principal problem here is that your are doing your setup and
simulation with non-AMBER software. This makes is rather difficult
to see whether what you see is indeed a matter of the force field
(pyrophosphates have certainly been done multiple times before) or this
is a matter how you use those programs or if those programs have a

Do you observe the same distortions in solution or in vacuo, that is
not bound to the protein? I think acpype is essentially just a wrapper
around antechamber and leap. A look into what that program does is
certainly a start too, e.g. does acpype keep all intermediary files it
generates so that you can see what it did.


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Received on Wed Jan 13 2016 - 07:30:03 PST
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