Dear Mr. Case,
Here is the content of the pdb file I am using:
-----------------------
HEADER CSD ENTRY CYTIDI10
COMPND UNNAMED
AUTHOR GENERATED BY CONQUEST
CRYST1 13.991 14.786 5.116 90.00 90.00 90.00 P 21 21 21 4
ATOM 1 C1 UNK 0 1 -7.625 2.311 2.861 1.00 0.00
ATOM 2 C2 UNK 0 1 -6.591 3.639 1.072 1.00 0.00
ATOM 3 C3 UNK 0 1 -7.828 0.195 3.843 1.00 0.00
ATOM 4 C4 UNK 0 1 -8.358 0.117 2.407 1.00 0.00
ATOM 5 C5 UNK 0 1 -5.345 1.801 1.954 1.00 0.00
ATOM 6 C6 UNK 0 1 -8.737 1.551 2.142 1.00 0.00
ATOM 7 C7 UNK 0 1 -4.344 2.055 1.091 1.00 0.00
ATOM 8 C8 UNK 0 1 -6.854 -0.895 4.219 1.00 0.00
ATOM 9 C9 UNK 0 1 -4.484 3.157 0.205 1.00 0.00
ATOM 10 H1 UNK 0 1 -3.470 1.582 1.136 1.00 0.00
ATOM 11 H2 UNK 0 1 -8.758 1.804 1.079 1.00 0.00
ATOM 12 H3 UNK 0 1 -8.535 0.074 4.497 1.00 0.00
ATOM 13 H4 UNK 0 1 -7.597 -0.163 1.821 1.00 0.00
ATOM 14 H5 UNK 0 1 -8.017 3.209 3.213 1.00 0.00
ATOM 15 H6 UNK 0 1 -5.345 1.065 2.604 1.00 0.00
ATOM 16 H7 UNK 0 1 -3.610 4.184 -1.330 1.00 0.00
ATOM 17 H8 UNK 0 1 -2.812 3.135 -0.604 1.00 0.00
ATOM 18 H9 UNK 0 1 -9.122 -1.686 2.164 1.00 0.00
ATOM 19 H10 UNK 0 1 -6.086 -1.730 2.619 1.00 0.00
ATOM 20 H11 UNK 0 1 -10.297 1.316 3.157 1.00 0.00
ATOM 21 H12 UNK 0 1 -7.401 -1.819 4.374 1.00 0.00
ATOM 22 H13 UNK 0 1 -6.254 -0.518 5.039 1.00 0.00
ATOM 23 N1 UNK 0 1 -5.560 3.946 0.238 1.00 0.00
ATOM 24 N2 UNK 0 1 -6.469 2.580 1.948 1.00 0.00
ATOM 25 N3 UNK 0 1 -3.538 3.464 -0.680 1.00 0.00
ATOM 26 O1 UNK 0 1 -7.183 1.486 3.919 1.00 0.00
ATOM 27 O2 UNK 0 1 -7.640 4.312 1.075 1.00 0.00
ATOM 28 O3 UNK 0 1 -9.991 1.919 2.710 1.00 0.00
ATOM 29 O4 UNK 0 1 -9.441 -0.772 2.244 1.00 0.00
ATOM 30 O5 UNK 0 1 -5.844 -1.110 3.269 1.00 0.00
CONECT 1 6 14 24 26
CONECT 2 23 24 27
CONECT 3 4 8 12 26
CONECT 4 3 6 13 29
CONECT 5 7 15 24
CONECT 6 1 4 11 28
CONECT 7 5 9 10
CONECT 8 3 21 22 30
CONECT 9 7 23 25
CONECT 10 7
CONECT 11 6
CONECT 12 3
CONECT 13 4
CONECT 14 1
CONECT 15 5
CONECT 16 25
CONECT 17 25
CONECT 18 29
CONECT 19 30
CONECT 20 28
CONECT 21 8
CONECT 22 8
CONECT 23 2 9
CONECT 24 1 2 5
CONECT 25 9 16 17
CONECT 26 1 3
CONECT 27 2
CONECT 28 6 20
CONECT 29 4 18
CONECT 30 8 19
MASTER 0 0 0 0 0 0 0 0 30 0 30 0
END
-------------------------------------------
When I use Molden/Insight 2/Maestro, the structure is ok.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
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---------------------------------------------------------------
On Tue, 20 Apr 2004, David A. Case wrote:
> On Tue, Apr 20, 2004, Ilyas Yildirim wrote:
> >
> > After using gaussian, I checked out the result in MOLDEN. The molecule is
> > on a 2-D surface, not in a 3-D.
>
> Yes--the x-coordinate of every atom is 1.0; that will put things in a plane.
>
>
> > I do not understand why this happens.
>
> Nor do I, and I have not real way of knowing how/why that happened, since I do
> not know how you created your Gaussian input file.
>
> > The .pdb file I am using is either a cytosine or isocytosine taken from CCD
> > database.
>
> Are you sure this is in a correct PDB format?
>
> ...dac
>
>
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Received on Tue Apr 20 2004 - 22:53:00 PDT
