Is the water at the end of the system? Meaning after all solutes, ions etc
On Tue, Aug 15, 2023, 5:19 PM Derek M Shore via AMBER <amber.ambermd.org>
wrote:
> Hi Amber community,
>
> I’m trying to take a system that came from an openMM simulation and run it
> with Amber 2022 (using the CHARMM36 FF). To do this, I’m using CHARMM-GUI’s
> “Force Field converter”—not to switch force fields, but just MD engine file
> formats, input files, etc. The output of “Force Field converter” is a set
> of input files that enables you to minimize & equilibrate your system
> before production.
>
> I’ve used this for several systems, and it generally works great. However,
> for systems (typically those with a lot of waters), I get this error during
> the first minimization:
>
> Error: Fast 3-point water residue, name and bond data incorrect!
>
> Other users have posted that this can be due to an incorrectly set watnam
> or owtnm, however my system has the default WAT O H1 H2.
>
> Regardless, when I try changing watnam, I get this message:
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = 0.00000000
> Forcing neutrality...
>
> This seems to suggest that it’s not a problem with watnam, but something
> else.
>
> Interestingly, when it doesn’t find waters, the minimization runs without
> a problem.
>
> Finally, the system runs in openMM, so I doubt there is a problem with the
> system.
>
> Any idea why I might be getting the “fast 3-point water” error?
>
> Thanks very much!
> Derek
>
> Derek M. Shore, Ph.D.
> Lecturer of Physiology and Biophysics
> Scientific Computing Technology Engineer
> Institute for Computational Biomedicine
>
> Weill Cornell Medicine
> Department of Physiology and Biophysics
> 1300 York Avenue, Room LC501A
> New York, NY 10065
> des2037.med.cornell.edu<mailto:des2037.med.cornell.edu>
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Received on Wed Aug 16 2023 - 07:30:02 PDT
