g_mindist in 4.0.4 produces weird results
Analyzing a transient protein complex (chain A with residue 1-110 and B resid 111-199), I get weird results:
I am using option -or: "With -or, minimum distances to each
residue in the first group are determined and plotted as a function of
echo -e "chA\nchB\n"|g_mindist -or chAbyres.xvg
echo -e "chB\nchA\n"|g_mindist -or chBbyres.xvg
The last residue of chB always has a very low distance (0.09nm) which I can't observe in the simulation e.g. with vmd, and from how I understand this tool - there should be a residue on the other chain with the same (minimum) distance.
Here's what I did to check:
g_mindist of chain A / B / r_199 with -pi (periodic images). Looks fine, distances are > 3nm
chain A vs r_199 gives me the same results as chA vs chB
Any ideas what could be wrong?