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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>
>
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Received on Thu Nov 02 2017 - 22:00:03 PDT
