Dear Sir or Madam,
I am trying to extract hydrogen bonds within the first and second
hydration shells around the tetraphenylborate anion. I have used the
following cpptraj commands: radial, watershell, closest, and hbond. From
the RDF curve, I identified the first minima at 6.5 and 9.6 Å. When
using the solute center option, the distances are calculated from the
geometric center.
However, in subsequent steps with the watershell and closest commands,
it appears that distances are not measured from the geometric center or
center of mass. Instead, they seem to follow a nearest-solute-atom
approach. As a result, when I visualize the selected water molecules,
they appear at significantly larger distances when measured from the
center (e.g., the boron atom).
Is it possible to configure the watershell and closest commands to use
the center of mass instead? If so, how can this be achieved?
Thank you in advance for your help.
Best regards,
Ivana Nikšić-Franjić.
--
Ivana Nikšić-Franjić
Institut Ruđer Bošković$Bijenička cesta 54$10000 Zagreb$Croatia
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Received on Wed Mar 18 2026 - 06:00:02 PDT
