Alan,
Hydrogen is misssing on C4
otherwise your molecule must be with odd number of electrons adn therefore
with open shell
zoran
----- Original Message -----
From: "Alan" <alanwilter.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, April 12, 2010 5:29 PM
Subject: Re: [AMBER] trying to use antechamber with -nc 0 for a molecule
> Thanks dear Case.
>
> To be honest, I did not understand well your words. I am likely missing
> something else from my Chem classes.
>
> To add something else, here goes a picture of the 4 ligands I am trying to
> work with (in attach.).
>
> Lig. 2 and 3 worked fine with antechamber.
>
> Thanks,
>
> Alan
>
> On Mon, Apr 12, 2010 at 15:23, case <case.biomaps.rutgers.edu> wrote:
>
>> On Mon, Apr 12, 2010, Alan wrote:
>> >
>> > HETATM 759 O1 MOL 1 30.900 25.892 20.427 1.00 0.00
>> > HETATM 760 N1 MOL 1 31.331 26.323 21.712 1.00 0.00
>> > HETATM 761 O2 MOL 1 30.655 27.390 22.350 1.00 0.00
>> > HETATM 762 C1 MOL 1 32.091 25.503 22.441 1.00 0.00
>> > HETATM 763 C2 MOL 1 31.844 25.301 23.730 1.00 0.00
>> > HETATM 764 H1 MOL 1 30.874 25.361 24.226 1.00 0.00
>> > HETATM 765 N2 MOL 1 33.000 24.989 24.302 1.00 0.00
>> > HETATM 766 C3 MOL 1 33.938 24.991 23.361 1.00 0.00
>> > HETATM 767 C4 MOL 1 35.434 24.817 23.685 1.00 0.00
>> > HETATM 768 N3 MOL 1 33.383 25.279 22.180 1.00 0.00
>> > HETATM 769 C5 MOL 1 34.050 25.098 20.854 1.00 0.00
>> > HETATM 770 C6 MOL 1 34.970 26.276 20.500 1.00 0.00
>> > HETATM 771 O3 MOL 1 34.178 27.330 19.950 1.00 0.00
>> > HETATM 772 H2 MOL 1 34.118 28.084 20.607 1.00 0.00
>> > HETATM 773 H3 MOL 1 33.261 25.049 20.104 1.00 0.00
>> > HETATM 774 H4 MOL 1 34.640 24.182 20.894 1.00 0.00
>> > HETATM 775 H5 MOL 1 35.756 26.002 19.796 1.00 0.00
>> > HETATM 776 H6 MOL 1 35.433 26.666 21.407 1.00 0.00
>> > HETATM 777 H7 MOL 1 36.170 24.824 22.882 1.00 0.00
>> > HETATM 778 H8 MOL 1 35.756 24.686 24.719 1.00 0.00
>> >
>> > INFO: Number of electrons is odd: 89
>>
>> Your molecule has a weird geometry around atom C4, and an add number of
>> electrons with neutral charge. Antechamber only works on closed shell
>> molecules.
>>
>> ...dac
>>
>>
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>>
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
>
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Received on Mon Apr 12 2010 - 09:00:04 PDT
