On 6/27/12 11:08 AM, reising...@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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