[gmx-users] problem

Alex 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.


More information about the gromacs.org_gmx-users mailing list