[gmx-users] #coordinates do not match

The One And Only chappyboy29 at gmail.com
Sun Aug 25 06:04:34 CEST 2013

I've tried the same process twice to two different proteins, but still got
the same error that the #coordinates in the topology file did not match the
#coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is
the process I went through:

*pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -ignh*

*grompp -f minim.mdp -c 1xyw.gro -p 1xyw.top -o 1xyw-EM-vacuum.tpr*

*mdrun -v -deffnm 1xyw-EM-vacuum -c 1xyw-EM-vacuum.pdb -pd*

*editconf -f 1xyw-EM-vacuum.pdb -o 1xyw-PBC.gro -bt dodecahedron -d 1.0*

*genbox -cp 1xyw-PBC.gro -cs spc216.gro -p 1xyw.top -o 1xyw-water.pdb*

*grompp -v -f minim.mdp -c 1xyw-water.pdb -p 1xyw.top -o 1xyw-water.tpr*

*genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname
NA -nname CL*

*grompp -v -f minim.mdp -c 1xyw-solvated.pdb -p 1xys.top -o

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