When I loadmol2 on that mol2 it doesn't show the atoms. Odd that build
in leap left it planar, worth having a developer look at.
Bill
On 11/2/17 10:11 PM, Shilpa Gupta wrote:
> 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 - 23:00:03 PDT
