Error on psf generation

HADDOCK
1

Hi Alex,
I’m trying to dock a ligand using a topology from acpype

At the stage of generating the psf I get the following error (below), for the atoms in a cyclopropyl group, about a dihedral where the first and last atom are the same (so I guess this dihedral doesn’t really make sense)

This dihedral is not in the ligand topology that I’m providing, is it autogenerated?
Settting: “autogenerate angles=True dihedrals=False end” in the ligand.top doesn’t solve it.

I can work around it by adding a cx_ cx_ cx_ cx_ dihedral to the topology, but
any suggestion how to best handle this?

Eiso

%CODDIH-ERR: missing dihedral parameters %%%%%%%%%%%%%%%%%%%%%
  dihedral energy constant missing.
  target dihedral value missing.
  periodicity missing.
  ATOM1: SEGId="    ",  RESId="502 ",  NAME="CI2 ",  CHEMical="CX_ "
  ATOM2: SEGId="    ",  RESId="502 ",  NAME="CZ  ",  CHEMical="CX_ "
  ATOM3: SEGId="    ",  RESId="502 ",  NAME="CI1 ",  CHEMical="CX_ "
  ATOM4: SEGId="    ",  RESId="502 ",  NAME="CI2 ",  CHEMical="CX_ "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODDIH-ERR: missing dihedral parameters %%%%%%%%%%%%%%%%%%%%%
  dihedral energy constant missing.
  target dihedral value missing.
  periodicity missing.
  ATOM1: SEGId="    ",  RESId="502 ",  NAME="CI1 ",  CHEMical="CX_ "
  ATOM2: SEGId="    ",  RESId="502 ",  NAME="CZ  ",  CHEMical="CX_ "
  ATOM3: SEGId="    ",  RESId="502 ",  NAME="CI2 ",  CHEMical="CX_ "
  ATOM4: SEGId="    ",  RESId="502 ",  NAME="CI1 ",  CHEMical="CX_ "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODDIH-ERR: missing dihedral parameters %%%%%%%%%%%%%%%%%%%%%
  dihedral energy constant missing.
  target dihedral value missing.
  periodicity missing.
  ATOM1: SEGId="    ",  RESId="502 ",  NAME="CZ  ",  CHEMical="CX_ "
  ATOM2: SEGId="    ",  RESId="502 ",  NAME="CI1 ",  CHEMical="CX_ "
  ATOM3: SEGId="    ",  RESId="502 ",  NAME="CI2 ",  CHEMical="CX_ "
  ATOM4: SEGId="    ",  RESId="502 ",  NAME="CZ  ",  CHEMical="CX_ "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODDIH error encountered: program will be aborted.
   (CNS is in mode: SET ABORT=NORMal END)
2

Hi Eiso

You are as good an expert as us on this :slight_smile:

This dihedral is not in the ligand topology that I’m providing, is it autogenerated?

Settting: “autogenerate angles=True dihedrals=False end” in the ligand.top doesn’t solve it.

I can work around it by adding a cx_ cx_ cx_ cx_ dihedral to the topology, but
any suggestion how to best handle this?

These are weird dihedrals involving twice the same atom…

Out of curiosity, did you try submitting it to the HADDOCK server to see if it can handle it?