nedomacho at gmail.com
Sun Sep 23 01:54:21 CEST 2018
> This generic warning shows up for any program that uses atomic radii
> but has not been provided a .tpr file, which contains unambiguous
> masses and atom types. The warning just alerts the user to the
> possibility that something strange might happen when guessing what an
> atom is based solely on its name. For example, "CA" is often the
> alpha-carbon in proteins, but could it be a calcium ion in some cases?
> Similarly, is "HG" a hydrogen at the gamma-position or is it mercury?
Since we supply the topology file, I thought, this gave a way for the
utility to look up pretty much everything. If it makes guesses in
absence of a tpr, it could potentially result in overlap issues when you
have systems with e.g. LJ parameters that are far from anything else in
Gromacs. In my case sometimes, big fat molybdenum atoms. I never
encountered any problems, but given what you said, might be possible.
In any case, thanks.
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