ah yes, that's true that the libraries in leap use internal coordinates for
the L version.
Not sure how to fix that easily, in the past I'd let leap build it and
apply strong restraints to the heavy atoms and minimize.
carlos
On Fri, Apr 2, 2021 at 4:26 PM gard nelson <aplaceforwhatnot.gmail.com>
wrote:
> Hi Carlos,
>
> Thanks for the quick reply. Sorry I wasn't more clear. The problem I'm
> having is with tleap adding hydrogens using implicit coordinates. The
> coordinates I'm starting from only have heavy atoms. Swapping the PHI terms
> in the implicit coordinates for HA and CB was enough to get tleap to put HA
> in the correct place for 17 amino acids, but for 3, including D-Thr, it
> puts HA and HB in the wrong places. Unfortunately, the spot it puts them in
> seems to be closer to the L torsion value so I often end up with an L-amino
> acid after minimization for those three. Like you said, the parameters work
> fine once I've got the right conformation. I'm investigating other methods
> for adding those hydrogens to the structure, but I'd like to understand
> where I'm going wrong with tleap and my internal coordinates too!
>
> Thanks!
> Gard
>
> >Hi Gard,
> >I'm not sure exactly what you need to do. Our "SB" force fields (ff99SB,
> >ff14SB, ff19SB) are equally applicable to L and D amino acids, and you
> just
> >need to use the modified coordinates. It sounds like you already found a
> >way to do that, so you should be ready to go. You do not need to generate
> >parameters.
> >For an example with ff14SB, see this paper:
> >
> >Experimental and Computational Analysis of Protein Stabilization by
> >Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded
> State
> >Effects. Zou, J., Song, B., Simmerling, C., Raleigh, D., Journal of the
> >American Chemical Society, 2016, 138 (48), 15682?15689
> >https://doi.org/10.1021/jacs.6b09511
> >
> >On Fri, Apr 2, 2021 at 2:15 PM gard nelson <aplaceforwhatnot.gmail.com>
> >wrote:
> >
> >> Hi everyone,
> >>
> >> I need to be able to build and simulate D amino acids so I made a new
> >> version of amino12.in. I have structures of the D amino acids heavy
> atoms,
> >> so I just need to add hydrogens and generate the parameters. With the
> >> exception of Pro, all I did was to swap the PHI(I) terms
> >> <https://ambermd.org/doc/prep.html> for HA and CB to get the correct
> >> chirality when adding hydrogens. For most of the residues, this works
> fine
> >> and I get a model that has H?s in all the right spots and runs just
> fine.
> >> However, for three residues, tleap adds HA and HB nearly on top of their
> >> neighboring atoms. (for D-Thr: N and OG1, respectively)
> >>
> >> I?ve copied my entry for D-Thr at the end. (modified values in *bold*)
> >> Interestingly, the HB-CB-CA-N dihedral, which should have a value of
> ~180
> >> degrees, is built with a value of ~60 degrees. I found that setting the
> >> PHI(I) term for HA to 180 and for HB to 45 got those Hs in about the
> right
> >> positions, but for some reason, changing the HA value affected the
> >> placement of H, which I would not have expected since H?s position
> should
> >> depend only on the dummy atoms. (How are the dummy atoms placed?)
> >>
> >> I?m obviously missing something about how these files work and/or
> interact
> >> with other configuration files. Thanks for helping me figure out what
> I?m
> >> doing wrong.
> >>
> >> Thanks!
> >>
> >> Gard
> >>
> >>
> >> D-THREONINE
> >>
> >> DTH INT 1
> >> CORR OMIT DU BEG
> >> 0.00000
> >> 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
> >> 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
> >> 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
> >> 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
> >> 5 H H E 4 3 2 1.010 119.800 0.000 0.27190
> >> 6 CA CX M 4 3 2 1.449 121.900 180.000 -0.03890
> >> 7 HA H1 E 6 4 3 1.090 109.500 *60.000*
> 0.10070
> >> 8 CB 3C 3 6 4 3 1.525 111.100 *300.000*
> 0.36540
> >> 9 HB H1 E 8 6 4 1.090 109.500 180.000 0.00430
> >> 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 -0.24380
> >> 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.06420
> >> 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.06420
> >> 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.06420
> >> 14 OG1 OH S 8 6 4 1.430 109.470 60.000 -0.67610
> >> 15 HG1 HO E 14 8 6 0.960 109.470 180.000 0.41020
> >> 16 C C M 6 4 3 1.522 111.100 180.000 0.59730
> >> 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790
> >>
> >> IMPROPER
> >> -M CA N H
> > CA +M C O
> >>
> >> DONE
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> >
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Received on Fri Apr 02 2021 - 14:30:02 PDT
