Hi,

Sounds like you're trying to mix the input of two packages that may not
have been designed to work together. Don't do that. The warning that the
files have atoms that are ordered differently surely heralds disaster if
you were to proceed.

Mark

On Tue, Feb 20, 2018, 07:39 abhisek Mondal <abhisek.m...@gmail.com> wrote:

> Hi,
>
> I'm getting an unusual warning whenever I execute *$ grompp -f em.mdp -c
> solv.gro -p topol.top -o ions.tpr *
> saying:
>
>
> *Warning: atom name 4687 in topol.top and solv.gro does not match (C1B -
> N7N)*
> *.....*
> *......*
> *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*
>
> *INDIA*
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