yes i have selected all the atoms and then build in xleap. I have attached
the mol2 file generated after running antechamber, total number of bonds
are 6 in the mol2 file.
Shilpa
On 3 November 2017 at 10:25, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Had you selected all atoms and done a build in xleap, the molecule
> wouldn't be flat and the double bonds would have served their purpose.
>
> Bill
>
>
> On 11/2/17 9:48 PM, Shilpa Gupta wrote:
> > Thank you for the reply. One more thing the sqm.pdb which is generated
> > after running antechamber, should i use this pdb. sqm.pdb have non zero
> > coordinates whereas the pdb generated from xleap have zero z coordinates.
> >
> >
> > On 3 November 2017 at 10:06, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> 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 - 22:30:02 PDT
