I apologize for the typos, I was tired last nite :-) ...
I meant R-O-PO3 (2-), where the three terminal oxygens are equivalent and
are all the same charge because of resonance delocalization.
The amber99 atom types are R-OS-P(O2)3
The amber99 bond lengths are:
OS-P 1.622 angstroms
P-O2 1.480 angstroms for each of the three P-O2 bonds
note the longer bond length for the OS-P single bond.
Hope this helps, and sorry for the confusion!
Dean
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Fri Apr 16 2010 - 09:30:02 PDT
