[gmx-users] #coordinates do not match

[The One And Only]

How do you decrease the number of solvent molecules in a topology file? I
think this will solve my problem.


On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Hi,
> 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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