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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 19 17:09:11 CEST 2013

Hi Shahab,

You edited the .gro file, but you made an error. So you have to read the
manual to understand the file format and then see where and how your edited
file doesn't match.



On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati
<shahab.shariati at gmail.com>wrote:

> 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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Tsjerk A. Wassenaar, Ph.D.

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