[gmx-users] error in grompp
jalemkul at vt.edu
Mon Oct 8 02:56:52 CEST 2012
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.
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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