I don't think leap should change this, what enantiomers are in the input
pdb? Did leap change them? If so, which atoms got moved?
On Tue, Sep 5, 2023, 4:41 PM Todd Minehardt via AMBER <amber.ambermd.org>
wrote:
> I am constructing prepi and frcmod files from a PubChem 3D sdf file for a
> positively-charged (+1) S enantiomer. I do this by running antechamber and
> parmchk2:
>
> antechamber -fi sdf -i compound.sdf -fo prepi -o compound.prepi -nc 1 -seq
> y -j 5 -rn LIG -c bcc
>
> parmchk2 -f prepi -i compound.prepi -o compound.frcmod
>
> I have a nice clean PDB structure in which there are two occurences of the
> heavy atoms of LIG.
>
> When I run this through tLEaP, one LIG is S and the other is R (after
> using ambpdb for generating PDB from saved .prmtop and .crd files).
>
> Is there an explanation for this behavior, as it is repeatable; and I'm
> not doing anything at all to the compound.sdf file and only removed
> unwanted waters and the like from the PDB file from RCSB.
>
> Thank you,
>
> Todd Minehardt
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Received on Tue Sep 05 2023 - 14:30:02 PDT
