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

shahab shariati shahab.shariati at gmail.com
Thu Sep 19 17:00:03 CEST 2013

Dear Tsjerk

Thanks for your consideration.

I ignored Warning 1.

> 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

Based on your suggestion, I checked non-matching
atom names between topol.top and system.gro files.

I corrected system.gro file accordance with topol.top file.

I did this work very carefully. I was watchful to not
disturb the format of the system.gro file, so that when I saw
system gro file (before and after the correction) by an editor
program, both of them were same.

But, when I use grompp, I encountered with:

Fatal error:
Something is wrong in the coordinate formatting of file sys.gro.
Note that gro is fixed format (see the manual).

How to solve this problem?

Any help will highly appreciated.

Best wishes for you.

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