Dear amber users,
I am trying to calculate charges (with RESP) for
mdified T base. But, before getting to modifed base I
decided to generate charges for T base to make sure I
get same (or similar) charges as reported in
all_nucleic94.in
I ran Gaussian98 on DT fragment from all_nucleic94.in
without PO2 group. H was added to O5' and O3'. I got
potential points, and ran 2stage RESP (inputs below).
Below is a charge comparison table. Resulting charges
are quite different especially O5' and C5.
What could be the problem? Am I using right theory and
basis sets? Are my RESP inputs correct or am I missing
something?
Thanks in advance.
Eva.
----------------------
Charge comparison
----------------------
DT(all_nucleic94) B3LYP 6-31G HF 6-31G*
q q q
O5' -0.4954 -0.626484 -0.622266
C5' -0.0069 0.040536 0.023536
H5'1 0.0754 0.086212 0.083917
H5'2 0.0754 0.086212 0.083917
C4' 0.1629 0.025002 0.074593
H4' 0.1176 0.133059 0.128822
O4' -0.3691 -0.409543 -0.40243
C1' 0.068 0.180595 0.136904
H1' 0.1804 0.17946 0.206058
N1 -0.0239 -0.084344 -0.045939
C6 -0.2209 -0.126903 -0.167607
H6 0.2607 0.168199 0.211167
C5 0.0025 -0.014134 0.004446
C7 -0.2269 -0.080416 -0.116807
H71 0.077 0.037202 0.043528
H72 0.077 0.037202 0.043528
H73 0.077 0.037202 0.043528
C4 0.5194 0.483967 0.508715
O4 -0.5563 -0.526076 -0.552938
N3 -0.434 -0.448178 -0.466261
H3 0.342 0.338162 0.349087
C2 0.5677 0.563967 0.572012
O2 -0.5881 -0.56979 -0.595139
C3' 0.0713 0.343876 0.315779
H3' 0.0985 0.034544 0.036912
C2' -0.0854 -0.168798 -0.204296
H2'1 0.0718 0.05663 0.068841
H2'2 0.0718 0.05663 0.068841
O3' -0.5232 -0.692228 -0.670396
H51 0.433265 0.426122
H52 0.424972 0.413825
----------------------------------
RESP inputs for 2 stages
----------------------------------
1st stage 2nd stage
&cntrl &cntrl
nmol=1, qwt=0.0005,
iqopt=2, nmol=1,
qwt=0.001 ihfree=1
&end &end
1.0 1.0
DT_HF_noPO2
ivary=0 0 31
8 -99
6 0
1 0
1 3
6 -99
1 -99
8 -99
6 -99
1 -99
7 -99
6 -99
1 -99
6 -99
6 0
1 0
1 15
1 15
6 -99
8 -99
7 -99
1 -99
6 -99
8 -99
6 -99
1 -99
6 0
1 0
1 27
8 -99
1 -99
1 -99
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Received on Mon Oct 08 2001 - 14:44:16 PDT
