[gmx-users] error_in topology

balaji nagarajan balaji_sethu at hotmail.com
Mon Oct 10 12:00:27 CEST 2011

Dear Users ! 

I have a problem in generating the topology of the attached molecule as pdb.

earlier i have done using the same pdb for solvating the structure using spc and spce water box , 

there was no such error when i do for TIP4P and oplsaa force field i got the error 

as follows 

Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (1AKI_solv.gro, 4164)
             does not match topology (topol.top, 5527)

I used the following lines to do that 

pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em

in the grompp it says the error , how to solve this ,  and it comes only for tip4p not for other water models.

thanks in advance 
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