Dear Amber Comunity,
I have performed a test calculation using RED (Multi molecule - multi
reorientation RESP fit) for the 4 canonical RNA bases: RG, RA, RC and
RU. The starting point were canonical A-form nucleotides with C3'-endo
sugar pucker. I used 3 reorientations. The fit was performed as
described in the original paper of RESP, with all the sugar atoms but
C1' and H1' intermolecular fitted. Presumably using this protool I hoped
to reproduce the atomic charges on RN nucleotides that are currently
used in amber. To my surprise there are striking differences sometimes
(especially on purines). Some time ago Francois told me that acceptable
differences are in the range of 0.07. I checked the input and I
calculated the charges for single nucleotides and I concluded that there
is nothing wrong with my inputs. I will list below the results on the
base atoms using wonder marks where I found differences (I tolarated a
difference up to 0.03-0.04). Now, the question that I have is: Should we
worry about these differences??? Has somebody of you ever tried to do
this calculation? If yes ... are your data fitting mine or the Amber
better?
I am fighting in getting charges for some base analogues. I tried -CH3
instead of sugar but it is clear that this is not a good approach
because the differences between the charges from entire nucleodies
differ significantly. My ideea was now to fit all these new bases with
the existing RNA bases and that's why I performed this test
calculations. The problem with my analogues is that there is very litte
experimental information them and their behaviour in RNA. They are
fluorescent so they might be interesting for the future. I also dont
have too much time to run MD simulations using these bases.
I am wondering if there is answer to this questions and also I am
wondering if these differences are observed...did someone ever thought
of changing the charges in Amber??
* For the calculation all nucleotides were optimized with G03 using
standard gaussian inputs (as described in RED)
Best regards
vlad
Results:
RU
Atom RU (amber) RU-6r Multi-RN
N1 0.0418 0.0408 0.0356
C2 0.4687 0.4956 0.4897
O2 -0.5477 -0.5813 -0.5779
N3 -0.3549 -0.3821 -0.3708
H3 0.3154 0.2999 0.2954
C4 0.5952 0.6093 0.6055
O4 -0.5761 -0.5908 -0.5914
C5 -0.3635 -0.3786 -0.3616
H5 0.1811 0.1919 0.1894
C6 -0.1126 -0.0679 -0.1000
H6 0.2188 0.1904 0.2036
RC
Atom RC(amber) RC-6r Multin-RN
N1 -0.0484 -0.0361 -0.0480
C2 0.7538 0.7667 0.7717
O2 -0.6252 -0.6490 -0.6489
N3 -0.7584 -0.7628 -0.7644
C4 0.8185 0.8077 0.8112
N4 -0.9530 -0.9498 -0.9445
H41 0.4234 0.3955 0.3917
H42 0.4234 0.3955 0.3917
C5 -0.5215 -0.5363 -0.5413
H5 0.1928 0.2108 0.2112
C6 0.0053 0.0106 0.0398
H6 0.1958 0.2025 0.1747
RA
Atom RA RA-6r Multi-RN
N1 -0.7615 -0.7747 -0.7743
C2 0.5875 0.5683 0.5710
H2 0.0473 0.0428 0.0415
N3 -0.6997 -0.7346 -0.7355
C4 0.3053 0.4184 0.4235 !!!!!!!!!!!!
C5 0.0515 0.0114 0.0200
C6 0.7009 0.7043 0.6973
N6 -0.9019 -0.9070 -0.9136
H61 0.4115 0.3915 0.3947
H62 0.4115 0.3915 0.3947
N7 -0.6073 -0.5813 -0.5903
C8 0.2006 0.1649 0.1912
H8 0.1553 0.1763 0.1639
N9 -0.0251 -0.0314 -0.0428
RG
Atom RG RG-6r Multi-RN
N1 -0.4787 -0.5677 -0.5973 !!!!!!!!!!!!
H1 0.3424 0.3552 0.3608
N2 -0.9672 -0.9082 -0.9064 !!
H21 0.4364 0.3859 0.3833 !!
H22 0.4364 0.3859 0.3833 !!
C2 0.7657 0.7287 0.7628
N3 -0.6323 -0.6023 -0.6291
C4 0.1222 0.1904 0.1810 !!!!
C5 0.1744 0.1119 0.1109 !!!!
C6 0.4770 0.5746 0.5921 !!!!!!!!!!!!!!!!
O6 -0.5597 -0.5765 -0.5792
N7 -0.5709 -0.5622 -0.5690
C8 0.1374 0.1588 0.1589
H8 0.1640 0.1620 0.1637
N9 0.0492 0.0139 0.0478
--
Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49-551-201.1327
e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
home tel: ++49-551-9963204
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Received on Fri Sep 10 2004 - 14:53:00 PDT
