On Thu, Feb 03, 2022, Sam Walsworth (Researcher) wrote:
>It seems that the bonds I presumed were missing actually do exist in the
>prmtop file. The problem seems to occur when I convert this prmtop file
>(with the corresponding inpcrd file) into .gro and .top files for use
>in gromacs, again with ParmEd. The .top file contains all the bonds and
>parameters I need but loading the .gro into a couple different guis (PyMOL,
>jmol, vmd) all show that my silver containing bonds don't exist, and the
>silver atom is floating non-bonded in space.
Please be sure that the bonds are actually absent in the gromac topology
files; don't rely just on seeing bonds are "drawn" in some GUI program.
(Maybe you've already done this....)
....dac
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Received on Fri Feb 04 2022 - 06:00:02 PST
