Dear Homa,
Remember that phosphate is resonance delocalized, so all three oxygen atoms
of R-PO3 (3-) are identical and indistinguishable. Also all three O-P bonds
are of equal length.
Hope this helps.
Dean
> From: Homa Azizian <homa.azizian.anu.edu.au>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Thu, 15 Apr 2010 20:46:49 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] BOND TYPE
>
> Hi,
> after loadamber the prepin file, as I found that the charge on all 3 O of
> (phosphate group O=PO2), is equalI,I decided to change the order of one bond
> to double, with this command:
> bond CAP.P1 CAP.O8 "="
> but I got this error: bond Argument #1 is type string must be of type: [atom]
> I also add the number of atom according to the .prepin numbering but this
> error still exist.
> I searching the mailing list but still have problem
> Thank's
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Received on Thu Apr 15 2010 - 19:30:03 PDT
