[gmx-users] Creating .ndx for TIP5Pwater
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 20 08:14:57 CET 2007
> Dear David,
> I didn't get the desired box length when I tried to use editconf command
> ( I took the tip5p box from gromacs/tutor directory) . Then, I tried
> editconf command to generate .gro file using myown water box. It worked!!
> Still, there is a problem. How can I create .ndx file?- I tried
> make_ndx -n tip5p_W.pdb, but it resulted in a message: input/output error.
probably the pdb file doesn't exist or you're not allowed to write in
> Could you suggest an alternative way for builing up ndx files?
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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