[gmx-users] non-matching atom names

abhisek Mondal abhisek.mndl at gmail.com
Tue Feb 20 07:39:01 CET 2018


I'm getting an unusual warning whenever I execute *$ grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr *

*Warning: atom name 4687 in topol.top and solv.gro does not match (C1B -
*WARNING 1 [file topol.top, line 44227]:*
*  71 non-matching atom names*
*  atom names from topol.top will be used*
*  atom names from solv.gro will be ignored*

I'm having a protein ligand system, where topology of ligand (*ligand.itp*)
is generated from CGenFF and *ligand.gro* (for building the *complex.gro*) file
was obtained from PRODRG server.

Please suggest me a way out of this.

Thank you.

Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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