[gmx-users] Re: gro file formate error

Justin Lemkul jalemkul at vt.edu
Wed Oct 16 16:57:38 CEST 2013

Please keep all Gromacs-related correspondence on the gmx-users mailing list.  I 
am CC'ing this reply to the list and ask that all future discussion occur there.

On 10/16/13 9:47 AM, sunyeping wrote:
> Dear Dr. Lemkul,
> I am working with protein-ligand system and I have prepared the gro file of
> protein using pdb2gmx and gro file of the ligand by PRODRUG online servive. I
> paste the atom cooridnates of the ligand in the ligand gro file at the end of
> the protein gro file, just before the last line for box vector, but when I run
> editconf, I got the error message:
> Fatal error:
> Something is wrong in the coordinate formatting of file conf.gro. Note that gro
> is fixed format (see the manual)
> I cannot find the exact explanation about the gro file format, so could you help


> me with that? The attached file is the gro file that cause the error.

In the future, please provide a link to send files (via the mailing list).

Your file is completely misformatted, with columns misaligned and bizarre 
newline characters.  Be sure you are always using a plain text editor and that 
you use dos2unix if necessary.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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