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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Received on Fri Apr 02 2021 - 11:30:03 PDT
