Hi. I’m running into a problem when trying to do a protein-ligand docking on a local installation of Haddock3. My topoaa module is having issues with my pdb file. Upon examining the .out file, I find the following errors:
ASSFIL: file CI1011_CID_166558.pdb opened.
CHAIN>end
SEGMENT>
SEGMENT>coordinates @@$coor_infile
%SEGMENT-ERR: unrecognized command:
coordinates
^^^^^^^^^^^
ASSFIL: file CI1011_CID_166558.pdb opened.
%SEGMENT-ERR: unrecognized command:
delete
^^^^^^
%SEGMENT-ERR: unrecognized command:
delete sele=
And a few similar as it goes forward. I’ve been able to successfully run an example protein-ligand docking, so I’m unsure why this is only happening for my system. Any help would be greatly appreciated.
I’ve been trying to track down the problem, and I might have stumbled upon something related. In my .inp file for the ligand, The input structures has the line
eval ($ncomponents = 0)
I’m guessing for some reason this is the problem, but I’m not sure how to go about fixing this.
this is a problem we have encountered ourselves recently - the additional ligand parameters cause CNS to hit an array size limit.
This will require recompiling CNS.
We are looking into it to check if other parameter sizes need to be increased
Okay, thank you! Any suggestions on how to proceed in the mean time? Is this solved by recompiling CNS or will I need to wait for a solution?
What we found so far is that we are hitting the maximum number of atom types when adding several ligand parameters.
Recompiling CNS is not a big deal for us.
On what OS are you running haddock3?
It’s installed on an HPC cluster using Linux.
Try replacing your CNS executable by the following one:
https://surfdrive.surf.nl/files/index.php/s/o6BgQF6qVwHzbws
And let me know if this works.