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 - 12:00:03 PDT
