[AMBER] problem with heavy atom (Cl atom) of ligand in tleap

From: Seketoulie Keretsu <sekekeretsu.gmail.com>
Date: Fri, 27 Sep 2019 20:52:02 +0900

I am preparing parameters for protein ligand complex. The ligand has two
chlorine atoms and other heteroatoms. During parameter preparation using
tleap, when I load the complex.pdb (protein + ligand), I encounter the
following message, which subsequently leads to problem with topology and
parameter file generation. The system generated message is given below.

Warning: One sided connection. Residue (default_name) missing connect1 atom.
Created a new atom named: CL29 within residue: .R<UNK 1133>
Created a new atom named: CL35 within residue: .R<UNK 1133>
  Added missing heavy atom: .R<UNK 1133>.A<Cl35 17>
  Added missing heavy atom: .R<UNK 1133>.A<Cl29 6>
  total atoms in file: 2478
  Leap added 2389 missing atoms according to residue templates:
       2 Heavy
       2387 H / lone pairs
  The file contained 34 atoms not in residue templates

I have developed the library file (.lib), frcmod etc for the ligand as per
the sustiva tutorial.

How do i resolve this issue? Thank you. Regards.
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Received on Fri Sep 27 2019 - 05:00:01 PDT
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