[gmx-users] Creating .ndx for TIP5Pwater

[David van der Spoel]

JMandumpal wrote:
> 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 
this directory.

> 
> Could you suggest an alternative way for builing up ndx files?
> 
> regards
> Jestin
> 
> 
> 


-- 
David.
________________________________________________________________________
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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