[gmx-users] make index

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 17:13:06 CEST 2012

On 6/27/12 11:08 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I want to  make an index with "make_ndx".
> But when I just wanted to group SOL and CL   and   Protein and DPPC  it
> tells me when I want to run grompp afterwards that there are some residues
> not indexed.

Copying and pasting an error message is much more effective.  I could guess at 
what this error is, but seeing it would be more useful.

> I thought that that might be because the NA-ions are not grouped. But when
> I want to group them together with the SOL and the CL with the command
> 14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could
> not be found. That is reasonable since my group is called: NA_CL_SOL
> So my question is: how can I rename such a index group?

The names specified in the .mdp file and .ndx files must match, so you can 
either change the names in the .mdp file (easiest), use a text editor to modify 
the name of the group in the .ndx file (same principle, probably a little more 
scrolling and/or find and replace), or use make_ndx to rename the groups (not 
very efficient in this case).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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