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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Sep 27 2019 - 05:30:03 PDT
