HI
Just look at the atom names of the two atoms mentioned.
I guess the atom names in the lib are Cl29 and Cl35 (and not CL29 and CL35).
Best Regards
On Fri, 27 Sep 2019 at 17:07, Seketoulie Keretsu <sekekeretsu.gmail.com>
wrote:
> 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 - 05:00:02 PDT
