[gmx-users] error in grompp

Nur Syafiqah Abdul Ghani pqah123 at gmail.com
Mon Oct 8 02:42:37 CEST 2012

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

[ 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..

Thanks in advance!

Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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