Dear AMBER users,
I have been trying to grow side chains with leap given the backbone atoms
and a residue template file, but when measuring the dihedreal angle
connecting the side chain with the backbone it is not the one from the
template.
To be more specific let's take for instance a thymine DNA base. First I
have a pdb file with just the nucleotide backbone atoms (atoms 4-15 and
30-35) and also base atom N9 (atom 16), as well as a template like
"DT.in":
------------------------------------------------------------------------
0 0 2
D-THYMINE - with 5' - phosphate group and 3' - O(minus) group
DT INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000
2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000
3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000
4 P P M 3 2 1 1.60 119.04 200.00 1.1659
5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761
6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761
7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954
8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069
9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754
10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754
11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629
12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176
13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691
14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680
15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804
16 N9 N* S 14 13 11 1.53 109.59 -127.70 -0.0239
17 C8 CM B 16 14 13 1.37 123.04 81.59 -0.2209
18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607
19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025
20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269
21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770
22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770
23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770
24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194
25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563
26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340
27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420
28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677
29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881
30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713
31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985
32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854
33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718
34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718
35 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5232
CHARGE deoxy -resp T
1.1659 -0.7761 -0.7761 -0.4954 -0.0069
0.0754 0.0754 0.1629 0.1176 -0.3691
0.0680 0.1804 -0.0239 -0.2209 0.2607
0.0025 -0.2269 0.0770 0.0770 0.0770
0.5194 -0.5563 -0.4340 0.3420 0.5677
-0.5881 0.0713 0.0985 -0.0854 0.0718
0.0718 -0.5232
IMPROPER
C8 C2 N9 C1'
C4 C8 C5 C7
N9 N3 C2 O2
C5 N3 C4 O4
C2 C4 N3 H3
N9 C5 C8 H6
LOOP CLOSING EXPLICIT
C1' C2'
C2 N9
DONE
STOP
---------------------------------------------------------
When xleap adds the missing atoms it prints:
Added missing heavy atom: .R<DT 1>.A<C8 14>
Added missing heavy atom: .R<DT 1>.A<C2 25>
Added missing heavy atom: .R<DT 1>.A<C5 16>
Added missing heavy atom: .R<DT 1>.A<N3 23>
Added missing heavy atom: .R<DT 1>.A<O2 26>
Added missing heavy atom: .R<DT 1>.A<C7 17>
Added missing heavy atom: .R<DT 1>.A<C4 21>
Added missing heavy atom: .R<DT 1>.A<O4 22>
My questions are the following:
First, the order of adding the atoms doesn't correspond to the order in
the DT.in file.
Second, when I measure the dihedral angle defined by C8 N9 C1' O4'
it is not 81.59 as specified in line 17 above through atoms 17 16 14 13
but deviates by a few degrees.
All this seems to work much better with amino acids, but I don't know why.
Any comments and insights are very appreciated!
Best regards,
Robert
Received on Mon Apr 07 2003 - 19:53:01 PDT
