[gmx-users] problem with the index.ndx for EDS simulation

James Starlight jmsstarlight at gmail.com
Tue Oct 23 10:19:37 CEST 2012

Dear Gromacs Users!

I'd like to perform Essential Dynamics Sampling simulation in the
Contraction mode targeted to the active.pdb structure of my protein.
That X-ray structure lacks some atoms in comparison to the structure
of that proteins which I've used in My md run from which eigenvectors
for further biased MD run have been extracted.

So I create 2 index files: one for main-chain atoms of my full-length
structure which I've used in MD_run and another for the truncated
X-ray structure. Than I added main-chain sub-set atoms from second  to
first index.ndx.

than I've launched

make_edi -f EDA_eigenvec.trr -n index -s minim  -eig  EDA_eigenval.xvg
-radcon 1-30 -tar xz.pdb -o b2ar_eda_biased_targeted.edi

where minim.tpr is the topology for full-length structure
xz.pdb is the X-ray truncated structure
index is the merged index file

on the next step I've choise 2 groups- one for full structure and
another for x-ray truncated structure consisted of less number of

after that I've obtain error

Fatal error:
Couldn't find atom with index 1128 in structure xz.pdb

where the 1128 atom is the LAST atom in my xz.pdb structure which is
actuall present in both the index.ndx as well as in the xz.pdb

I've tried to repeat it on another atom subset ( e.g on C-alpha atoms)
and always obtain such error.

Why this occurs?

Thanks for help,


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