[gmx-users] .gro file problem

[Justin Lemkul]

On 10/28/12 12:57 PM, Albert wrote:
> hello:
>
>   I finished a MD and it generate a .gro file: confout.gro
>
> However, I find that there is some problems:
>
> editconf -f confout.gro -o md.pdb
>
> it said:
>
> Program grompp, VERSION 4.5.5
> Source code file: confio.c, line: 801
>
> Fatal error:
> Something is wrong in the coordinate formatting of file md.gro. Note that gro is
> fixed format (see the manual)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "If You Want Something Done You Have to Do It Yourself" (Highlander II)
>
>
> However, I can open it with VMD without no problem. But if I try to do it with
> gromacs, similiar errors happen.
>
> grompp -f myMD.mdp -c md.gro -p complex.top -o md2.tpr
> Program grompp, VERSION 4.5.5
> Source code file: confio.c, line: 801
>
> Fatal error:
> Something is wrong in the coordinate formatting of file md.gro. Note that gro is
> fixed format (see the manual)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Carry Me Away" (Motors)
>
>

Visual inspection with a text editor should tell you what's wrong.  Either the 
file is incomplete (i.e. header or box vectors missing) or the coordinates are 
large (indicating the system became unstable at some point).  The fact that VMD 
loads the file suggests that the latter may be true.  An incomplete file would 
not load, but one with screwy coordinates still would.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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