Dear AMBER users:
I am trying to simulate the interaction between a protein and mannose
and modifications of mannose. Since there are no parameters for these
modifications, I used antechamber for the generation of these
parameters. But when simulating the 6-amino-6-desoxy-mannose there seem
to be a strong interaction between the amino group (positively charged)
and the ring oxygen O5. During the simulation in a water box, the amino
group almost always points to O5. I would expect a more random
orientation of this group. Also the QM calculations imply that e.g. a
interaction of the amino group with O2 would be more favorable.
The charge of O5 is -0.47 (calculated using gaussian with the input file
provided by antechamber, the prep-file is given below). All the other
oxygens have much more negative partial charges in the range of -0.6 to
-0.7. Glycam assigns to the two lone-pairs of O5 in mannose a charge of
-0.167 resulting in a partial charge of -0.334, which is lower but not
so different to -0.47. Could somebody please help me finding the
problem, if there is one? Or is there a better method to get parameters
for modified sugar?
Thank you very much.
Thomas
MAN INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O4 oh M 3 2 1 1.540 111.208 180.000 -0.778455
5 H10 ho E 4 3 2 0.952 66.481 178.950 0.506526
6 C4 c3 M 4 3 2 1.412 49.348 -33.735 0.233728
7 H4 h1 E 6 4 3 1.083 110.029 -102.014 0.110380
8 C3 c3 M 6 4 3 1.517 111.932 18.649 0.124818
9 O3 oh S 8 6 4 1.405 106.033 -63.605 -0.701930
10 H9 ho E 9 8 6 0.949 110.926 156.986 0.470347
11 H3 h1 E 8 6 4 1.085 109.358 55.915 0.095003
12 C2 c3 M 8 6 4 1.529 108.636 176.185 0.172708
13 O2 oh S 12 8 6 1.393 110.698 63.270 -0.689865
14 H8 ho E 13 12 8 0.949 109.491 58.782 0.470134
15 H2 h1 E 12 8 6 1.085 110.078 -173.215 0.080913
16 C1 c3 M 12 8 6 1.526 109.979 -54.558 0.357225
17 O1 oh S 16 12 8 1.380 107.265 -68.717 -0.738510
18 H7 ho E 17 16 12 0.949 110.573 -163.393 0.493327
19 H1 h2 E 16 12 8 1.080 110.006 168.437 0.131496
20 O5 os M 16 12 8 1.409 111.533 52.933 -0.479735
21 C5 c3 M 20 16 12 1.391 115.742 -56.221 0.186918
22 H5 h1 E 21 20 16 1.088 110.818 -62.436 0.093007
23 C6 c3 M 21 20 16 1.527 104.591 179.725 0.038146
24 H6 hx E 23 21 20 1.079 111.141 -68.633 0.108432
25 H11 hx E 23 21 20 1.079 110.892 53.274 0.108432
26 N1 n4 M 23 21 20 1.508 110.091 172.656 -0.416481
27 H12 hn E 26 23 21 1.010 111.895 169.404 0.341145
28 H13 hn E 26 23 21 1.010 111.540 -70.186 0.341145
29 H14 hn E 26 23 21 1.019 109.284 47.901 0.341145
LOOP
C5 C4
IMPROPER
DONE
STOP
--
________________________________________________________________________________
Dr. Thomas E. Exner
Fachbereich Chemie
Universität Konstanz
78457 Konstanz
Tel.: +49-(0)7531-882015
Fax: +49-(0)7531-883587
Email: thomas.exner.uni-konstanz.de
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Received on Mon Aug 01 2011 - 06:30:04 PDT
