[gmx-users] Re: grompp for minimization: note & warning

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Sep 18 09:53:51 CEST 2013

Hi Shahab,

That site has a lot of structures. It would be better to explicitly state
which one you took. However, in this case, the better question is, how did
you write the topology, and did you check the correspondence of the order
of molecules/atoms in the topology file and the structure file? I guess the
answer to the latter is no...

> WARNING 1 [file topol.top, line 32]:
>   3632 non-matching atom names
>   atom names from topol.top will be used
>   atom names from system.gro will be ignored

Never ignore this warning, unless you understand why this is okay.



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