[gmx-users] Re: topology and coordinate file not matching after grompp

chinnu657 cma1g09 at soton.ac.uk
Wed Jul 31 17:29:52 CEST 2013

Hi Justin,
Oh, I see. I am going to paste my commands here. 

 pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
 pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
 editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0
 cat conf1.gro conf2.gro > system.gro
 genconf -f system.gro -o renumber.gro -renumber
 editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron
 genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro 
 grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr

It is after this that I get the error


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