In your PDB file, change atom names to CL29 to Cl29 and CL35 to Cl35.
This should solve your problem.
Best Regards
On Fri, 27 Sep 2019 at 17:49, Seketoulie Keretsu <sekekeretsu.gmail.com>
wrote:
> Hi, Thanks for the suggestion. Here below is the content of the .lib file.
> since GAFF uses lower case and ff99SB uses upper case, I am unsure what to
> expect. Please see the .lib file given below.
>
> !!index array str
> "ligand"
> !entry.ligand.unit.atoms table str name str type int typex int resx
> int flags int seq int elmnt dbl chg
> "Cl29" "cl" 0 1 131072 1 6 -0.093400
> "Cl35" "cl" 0 1 131072 2 6 -0.071400
> "C1" "ca" 0 1 131072 3 6 0.004400
> "C2" "ca" 0 1 131072 4 6 -0.108000
> "C3" "ca" 0 1 131072 5 6 -0.136000
> "C4" "ca" 0 1 131072 6 6 0.143600
> "C5" "ca" 0 1 131072 7 6 -0.136000
> "C6" "ca" 0 1 131072 8 6 -0.108000
> "N7" "nh" 0 1 131072 9 7 -0.727300
> "C8" "ca" 0 1 131072 10 6 0.724200
> "C9" "ca" 0 1 131072 11 6 -0.337200
> "C10" "ca" 0 1 131072 12 6 0.499200
> "N11" "nb" 0 1 131072 13 7 -0.767000
> "C12" "ca" 0 1 131072 14 6 0.897900
> "N13" "nb" 0 1 131072 15 7 -0.775000
> "N14" "nh" 0 1 131072 16 7 -0.657300
> "C15" "cc" 0 1 131072 17 6 -0.057700
> "C16" "cc" 0 1 131072 18 6 0.329200
> "N17" "nd" 0 1 131072 19 7 -0.511800
> Would appreciate if someone can give a hind to go forward. Thanks
>
> On Fri, Sep 27, 2019 at 8:52 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > 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 - 05:30:04 PDT
