[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

Justin Lemkul jalemkul at vt.edu
Wed Feb 27 16:14:35 CET 2013

On 2/27/13 10:03 AM, swati rana wrote:
> Hi all,
> After running the following command
> <b>perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5
> area.dat</b>
>   I modified the lipids in the topol.top file and in system.gro file the no
> of lipids and no of atoms respectively.
> but after that for energy minimization when i ran the following command:
> <b>grompp -f EM.mdp -c system.gro -p topol.top -o em.tpr</b>
> It is showing the following error. Please tell me if the command is right
> or not and if it is right then what can be done to resolve and why exactly
> it is showing this error. I checked the topology file but i am not able to
> reach any conclusion. Please guide me as most of you have faced this error
> and got the solution for it .
> <b>Ignoring obsolete mdp entry 'title'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> Generated 867 of the 1891 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> NOTE 1 [file topol.top, line 21239]:
>    System has non-zero total charge: 3.000002
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523
> Fatal error:
> number of coordinates in coordinate file (system.gro, 10019)
>               does not match topology (topol.top, 17093)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors</b>

Did you consult the website?  The answer is always the same...

If the numbers don't match, then your bookkeeping was incorrect.  Your topology 
specifies more atoms than your coordinate file, so you did not correctly account 
for the deletion of lipids or water.  Note that above, grompp is looking for 
SOL, but InflateGRO deletes all solvent from the input file, so you need to 
remove them from your topology as well.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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