[gmx-users] The loops run far away

[Tanping Li]

Dear all,

I am analyzing the interaction between a specific
residue and close residues. The residue is very close
to a loop (not the N and C terminal). I solvated the
protein several times, loops have different positions.
Sometimes, it goes far away from the crystal
structures. I tried my best to keep it around the
crystal position, but I can't. I have struggled for
two weeks. Any suggestions? I looked through the
mailing list, but can't find the related information.


Best
Tanping