Water in Sphere

[cwh.s...@gmail.com]

I am using a set of files produced by AmberTools.  When I start a waterswap calculation, I get a lot of messages about water.  Specifically "HOW IS THE MOLECULE OUTSIDE OF THE SPHERE? 16.0056 15"

Any help on what the issue is and how to fix would be appreciated.

[Christopher Woods]

  Hi,

The warning message relates to an issue with the reflection constraint being confused by some molecules on the boundary for some edge case confirmations. It is not something to be concerned about and the messages can be ignored. You should however make sure that you look at the PDB output files in, e.g. VMD, to make sure that the sampled conformations look good.

  Best wishes,

  Christopher

On 7 September 2017 at 22:50, <cwh.s...@gmail.com> wrote:

I am using a set of files produced by AmberTools.  When I start a waterswap calculation, I get a lot of messages about water.  Specifically "HOW IS THE MOLECULE OUTSIDE OF THE SPHERE? 16.0056 15"

Any help on what the issue is and how to fix would be appreciated.

--
You received this message because you are subscribed to the Google Groups "Sire Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sire-users+unsubscribe@googlegroups.com.
To post to this group, send email to sire-...@googlegroups.com.
Visit this group at https://groups.google.com/group/sire-users.
For more options, visit https://groups.google.com/d/optout.

--

---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com