Dear Dr. Bonvin and All,
I have two questions related to the errors that I m getting when I tried to submit job into HADDOCK guru interface.
Q1) I have followed the guru interface to dock a protein with organic ligand. I have changed ATOM tag to HETATM in ligand pdb. I followed exactly as guru interface tutorial based on abinitio method. When I tried to submit the job I got following error(bellow)?
Q2) I do have CSP(active residues) for the same protein(from NMR), when I used active residues for protein and left the passive residues as blank, the job didn’t get accepted and software was suggesting me to use active restraints for both protein and ligand. Is there is a way to use only protein CSP during docking (protein+ligand)?
Therefore, I would highly appreciate your help and valuable time, if you please suggest me how can I tackle this issue.
With many thanks
Vince
==================Error message===============================
ValueError: invalid literal for int() with base 10: ‘0.0’
Member initiosteps (number of MD steps for rigid body high temperature TAD) :
Invalid, optional
Exception:
Traceback (most recent call last):
File "/home/enmr/services/HADDOCK2.2/py/spyder/formtools/model.py", line 534, in _set
v = self._type(value)
ValueError: invalid literal for int() with base 10: ‘0.0’
Sounds like a typo when changing the number of steps… Make sure to enter only 0
Dear Dr. Bonvin,
As related to main post on protein+ligands docking in using guru interface.!!!
We have CSP (NMR) for the protein and I want to use as an active restraint input into guru interface(abinitio method). For the organic ligand we don’t have any restraints. What I did is I have added the active restraints for protein and I didn’t check the box to automatically define the passive residues for the protein(because i don’t have active restraints fro ligand). For the second molecule (ligand) I changed the ATOM tag to HETATM in pdb and I didn’t define both active and passive restraints. Software was complaining either I have to define active restraints for protein as well as to ligand or not to include restraints for both.
Q1: In guru interface based on abinitio docking is it possible to use CSP data of a protein alone?
Q2: Can I make the ligand as passive and restraints as 1,. Because I am considering ligand as one block.
Ligand pdb:
HETATM 1 O LIG 1 0.953 -0.161 0.057 0.00 0.00 O
HETATM 2 C LIG 1 2.147 0.067 -0.060 0.00 0.00 C
HETATM 3 C LIG 1 2.697 1.363 -0.642 0.00 0.00 C
Thank you in advance…
With many thanks
Vince
Use the second part of our online tutorial:
You can define the CSP residues for the protein, and the ligand should be active.