[gmx-users] Atom name mismatch between gro and top file

Dallas Warren dallas.warren at monash.edu
Thu Apr 11 09:15:44 CEST 2019

Simply change the order of the atoms in the gro file to match the topology

The order of the atoms is not in itself what is important, ie they can
really be in any order, it's that the names and order match between
coordinate - topology file and then within the topology file.

This error also typically shows up when the molecule list at the end of the
topology is different to how the molecules are ordered in the coordinate

For example coordinate file has 1x UNK, 1x SOL, 1x UNK then 3,000 SOL. A
topology with a list of the molecules as 2x UNK then 3,001x SOL will throw
up this error.

On Thu, 11 Apr. 2019, 3:00 pm RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:

> Hi Users.
> While doing protein-ligand simulation, I get a warning which state
> atom name mismatch between solv.gro and topol.top and name from top file be
> considered and gro will be ignored. Yes, there is a mismatch, as in gro
> file, the atom was in the order C-O-O and in itp file added to top, the
> order was O-C-O. the itp file was generated by prodrg server.
> 1. Is it fine to ignore the warning and continue with the simualtion?
> 2. If not, which file should i  rename? gro or itp?
> Thank you
> --
> *Regards,*
> *Rahul *
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