[gmx-users] error in grompp

[Justin Lemkul]

On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote:
> Dear All,
>
> Fatal error:
> number of coordinates in coordinate file (prot_wtr_solv.gro, 18031)
>               does not match topology (control.top, 16650)
>
> It happen when i started to minimize it by using the command
>
> grompp -v -f minim_first.mdp -p control.top -c prot_wtr_solv.gro -o
> minim_prot.tpr -zero
>
> When i open the control.top and the prot_wtr_solv.gro file and i
> startet to calculate the missing atom is about 1381 which is for my
> DRG molecule..
> I already edit and put the topology like below :
>
> ; Include topology for DRG
> #include "solvent.itp"
>
> [ system ]
> ; Name
> ALZHEIMER'S DISEASE AMYLOID in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DRG		               1381
> SOL                       350
>
> Can you guys please explain it to me why this happened..Its still cant
> be minimize it yet..
>

The answer to this error is always the same.

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to keep better track of the molecules in your system and adjust the 
topology accordingly.  When dealing with complex systems, you must do your own 
bookkeeping.

-Justin

-- 
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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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