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Dear Users ! <br><br>I have a problem in generating the topology of the attached molecule as pdb.<br><br>earlier i have done using the same pdb for solvating the structure using spc and spce water box , <br><br>there was no such error when i do for TIP4P and oplsaa force field i got the error <br><br>as follows <br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.3<br>Source code file: grompp.c, line: 523<br><br>Fatal error:<br>number of coordinates in coordinate file (1AKI_solv.gro, 4164)<br> does not match topology (topol.top, 5527)<br>--------------------------------------------------------------------<br><br>I used the following lines to do that <br><br>pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p<br>editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic<br>genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top<br>grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr<br>mdrun -v -deffnm em<br><br>in the grompp it says the error , how to solve this , and it comes only for tip4p not for other water models.<br><br>thanks in advance <br> </div></body>
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