[gmx-users] About ADP

[Daan van Aalten]

Hi Zhiguo

The server will do all this for you - just put in the heavy atom skeleton
without hydrogens or charges

Daan


On Sun, 14 Mar 2004, Zhiguo Liu wrote:

> Dear gmx-users £¬
>     I want to produce topol file of ADP with dundee server, what kind of protonate state should be choosed? that is, how many protons should be added to the negative "O" in "P-O-"?
>
>            _
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |
>          ...
>          (1)
>
>
>           OH
>           |  _
>         O=P-O
>           |
>           O
>           |  _
>         O=P-O
>           |
>           O
>           |
>          ...
>          (2)
>
>
> that equals to say, (1) or (2) should be choosed for the dundee server input?
>
>
> Best Regard!
>                                  Zhiguo Liu
>                                  DDDC
>                                  Chinese Academy of Science
>                                  Shanghai,China
>                                  zgliu at iris3.simm.ac.cn
>                                  2004-03-14
>
>
>
>
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##############################################################################
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk