On Thu, Oct 15, 2015 at 12:42 PM, MarcZhang <progress0935zhang.gmail.com>
wrote:
> Dear Amber user group
>
>
>
> I met a problem when I generated prmtop and inpcrp files for a complex
> system of a protein with coligand: Tetrabromobisphenol A (PDB ligand
> ID:XDI)
>
>
>
> I generated .lib and .frcmod for the coligand successively.
>
>
>
> However, tleap reported these lines when generating prmtop and inpcrp files
> for the complex system.
>
>
>
> Added missing heavy atom: .R<TBP 723>.A<BrAH 32>
>
> Added missing heavy atom: .R<TBP 723>.A<BrAG 27>
>
> Added missing heavy atom: .R<TBP 723>.A<BrAF 8>
>
> Added missing heavy atom: .R<TBP 723>.A<BrAE 4>
>
This means that LEaP found atoms that were in the residue template (TBP in
the .lib file) that were *not* in the PDB file. If this is expected, then
you can ignore this.
> Checking Unit.
>
> FATAL: Atom .R<TBP 723>.A<BRAE 33> does not have a type.
>
> FATAL: Atom .R<TBP 723>.A<BRAF 34> does not have a type.
>
> FATAL: Atom .R<TBP 723>.A<BRAG 35> does not have a type.
>
> FATAL: Atom .R<TBP 723>.A<BRAH 36> does not have a type.
>
This looks like the same atom names as above, but the R is upper-case
instead of lower-case. This suggests to me that your PDB file has atoms
named BRAE and BRAF instead of BrAE and BrAF (which are the names in the
.lib file). You must make these consistent.
> Checking parameters for unit 'Complex'.
>
> Checking for bond parameters.
>
> Could not find bond parameter for: ca -
>
> Could not find bond parameter for: ca -
>
> Could not find bond parameter for: ca -
>
> Could not find bond parameter for: ca -
>
This is weird. Maybe it's because not all atoms have a type? In any
case, make sure that the atom names in the PDB file match those in your
.lib file. And you can use parmchk2 to generate an frcmod file with all of
the parameters if you are still missing parameters after the above fixes.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 15 2015 - 10:30:05 PDT
