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 Tue Aug 15 2023 - 17:30:02 PDT
