[gmx-users] #coordinates do not match

rajat desikan rajatdesikan at gmail.com
Sun Aug 25 06:08:55 CEST 2013

In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral
-pname NA -nname CL* , you have not used -p 1xys.top   Consequently, I
don't think the ions are written into your .top . Please check and see if
grompp works.

On Sun, Aug 25, 2013 at 9:34 AM, The One And Only <chappyboy29 at gmail.com>wrote:

> 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
> 1xyw-EM-solvated.tpr*
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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