Hello,
I am trying to generate prep file of a molecule which has a chiral center.
Let the chiral carbon be X and four atoms attached to them are 1, 2, 3 and
4. all of these atoms are also has sidechains. Now after preparing the R
conformation prep file for the molcule I just interchanged the dihedral
angle collumn of the 2 and 3 atom. I could generate the topology, crd and
pdb files. Loading them with VMD shows different chirality for both of
them. However, interestingly, I can load pdb file of one using topology
file of another. Is that fine. I read about D amino acid in the amber forum
and it says that you only need to give the coordinate of D amino acid and
it loads with the topology of L amino acid provided. Now considering this I
tried to make a prep file for D leucine by just interchanging the dihedral
column of HA and CB as shown below (I call it Deucine and DEU)
DEUCINE
DEU INT 1
CORRECT OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.000
4 N n M 3 2 1 1.335 116.600 180.000 -.4937
5 H h E 4 3 2 1.010 119.800 0.000 .3018
6 CA c3 E 4 3 2 1.449 121.900 180.000 -.0097
7 HA h1 E 6 4 3 1.090 109.500 60.000 .0432
8 CB c3 3 6 4 3 1.525 111.100 300.000 -.1322
9 HB2 hc E 8 6 4 1.090 109.500 300.000 .0317
10 HB3 hc E 8 6 4 1.090 109.500 60.000 .0317
11 CG c3 3 8 6 4 1.525 109.470 180.000 .4429
12 HG hc E 11 8 6 1.090 109.500 300.000 -.0662
13 CD1 c3 3 11 8 6 1.525 109.470 60.000 -.4312
14 HD11 hc E 13 11 8 1.090 109.500 60.000 .1042
15 HD12 hc E 13 11 8 1.090 109.500 180.000 .1042
16 HD13 hc E 13 11 8 1.090 109.500 300.000 .1042
17 CD2 c3 3 11 8 6 1.525 109.470 180.000 -.4312
18 HD21 hc E 17 11 8 1.090 109.500 60.000 .1042
19 HD22 hc E 17 11 8 1.090 109.500 180.000 .1042
20 HD23 hc E 17 11 8 1.090 109.500 300.000 .1042
21 C c M 6 4 3 1.522 111.100 180.000 .6731
22 O o E 21 6 4 1.229 120.500 0.000 -.5854
LOOP
IMPROPER
-M CA N H
CA +M C O
DONE
STOP
However it is not loading with loadamberprep. Considering the similar idea
in case of my molecule it should have loaded. I don't know the mistake I am
doing. However, both my R and S configuration of the molecule I created
giving correct geometry. Thank you in advance for the suggestion.
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Received on Mon Jul 27 2015 - 10:00:02 PDT
