[gmx-users] problem with make_ndx

[Justin A. Lemkul]

Anushree Tripathi wrote:
> 
> Now, for making the index file it is showing option for DPPC but not for 
> Cl.The options which I found after running the command( i.e.,
> 
> make_ndx -f em.gro -o index.ndx)are given below:
> 
> 
>  0 System              : 17365 atoms
>   1 Other               :  6400 atoms
>   2 DPPC                :  6400 atoms
>   3 Water               : 10965 atoms
>   4 SOL                 : 10965 atoms
>   5 non-Water           :  6400 atoms
> 

If there's no CL ions (and you suspect there should be), then you've passed 
make_ndx a coordinate file that does not have CL in it.  Be careful with file 
names and use a text editor to examine the contents.

> 
> After following each and every step that you have given,when I run the command ( grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndp -o nvt.tpr).I am getting error:
> 
> number of coordinates in coordinate file (em.gro, 17365)
> 
> does not match topology (topol.top, 18379)
> 
> Please guide me.
> 

This error again suggests that you have not kept track of the contents of your 
coordinate file and/or topology and they now are not in sync with one another.

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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