Double bonds are not part of the Amber ff - they are only used
internally by leap to apply standard geometries when asked, which is
likely almost never.
Bill
On 11/2/17 9:19 PM, Shilpa Gupta wrote:
> Dear Amber Users,
> I have generated acetate structure using xleap I have drawn C double bond O
> but and then run antechamber. After the generation of mol2 or pdb(initial
> structure), both of them does not contain double bond and after running the
> antechamber sqm.pdb file is generated so, should i use that structure for
> further use or mol2 file generated.
> Thanks in advance.
>
>
>
> Shilpa Gupta
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Received on Thu Nov 02 2017 - 22:00:02 PDT
