Thank you very much for your answer.
Yes, I am using a local installation of Haddock.
Now, I have implemented all of your suggestions by adding to my protein PDB file several dummy atoms at the anticipated positions as inferred by the intramolecular PREs, e.g.: (ATOM 978 DUM DUM A 127 16.002 -11.515 -17.086 1.00 0.00). I made all the intermolecular restraints as ambiguous to all the dummy atoms, and added unambiguous intermolecular restraints to keep the positions of these atoms fixed relative to the protein position.
I have tried to run this as recommended, but unfortunately all of my trials were only running fine through the rigid-body stage, and all of them were failing at it1, always reporting the following error:
" -------------------------- Torsion Topology -----------------------------------
ERROR: A single-group tree does not have an
There are certain limitations with the current
implementation of torsion angle dynamics.
The problem is caused by isolated
(not covalently bonded) atoms.
We have made every effort to capture these
situations automatically. However, in some
cases you may still encounter this problem.
In order to fix this problem
(a) fix (fix atom selection) the offending
(b) if everything fails, use the Cartesian
%TORSION:TOPOLOGY error encountered: Fatal Topology Error
(CNS is in mode: SET ABORT=NORMal END)
ABORT mode will terminate program execution.
Program will stop immediately."
I tried to read through the online manual and the forum in order to get a proper fix for this issue.
So, I tried to set all the steps of it1 to 0, changed the dummy atoms into HETATM, and setting all of them to be fixed (simply by switching off the semi-flexible and fully-flexible options), but that did not resolve the issue.
I am not sure if I am missing something else.
It would be greatly appreciated if you help me figure out how to fix this problem.