I'm still not quite clear - what comes out of leap before anything else?
The atoms should match the input pdb, except for missing atoms (and then
you should get a warning in the leap log).
On Tue, Sep 5, 2023 at 6:43 PM Todd Minehardt <tminehardt.nobiastx.com>
wrote:
> Carlos,
>
> I've got a case where the neutrally-charged ligand heavy atoms are present
> in the PDB and are from the neutral S-enantiomer that was crystalized
> during experiment.
>
> I'm generating the +1 charged S enantiomer as prepi and frcmod files as
> described, and then assuming (perhaps incorrectly) that for each of the 2
> occurrences of LIG in the PDB that the requisite number of hydrogens -
> including the one that adds the +1 and the one that makes it the S
> enantiomer - get added.
>
> The initial structure (after solvation, neutralization, etc.) shows that
> the geometry of each of the LIGs is not quite right, but shakes out to one
> S and one R after minimization.
>
> Keep in mind that the LIG atoms are numbered in the PDB, and I'm going
> into this after removing CONECTs and inserting a TER card between the 2
> LIGs.
>
> I've already had issues with the GAFF atom types - which is expected - but
> am baffled to why, given one S enantiomer prepi/frcmod combo generated from
> the all-atom SDF from PubChem, the two LIGs shake out, as it were, to one S
> and one R.
>
> Note: the same system except with neutrally-charged S LIGs worked just
> fine - 2 starting S, 2 ending S after 100 ns.
>
> Help is much appreciated,
>
> Cheers,
>
> Todd
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Tuesday, September 5, 2023 4:23 PM
> *To:* Todd Minehardt <tminehardt.nobiastx.com>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] Chirality flipped for 2 identical molecules
>
> 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 - 17:00:02 PDT
