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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Nov 02 2017 - 22:00:03 PDT
