I think with VMD you can load the prmtop, which will tell it the bonds.
Bill
On 5/13/19 12:56 AM, Bill Ross wrote:
> If you want to see the bonds, perhaps those programs have a
> bondbydistance cmd like leap's? Or a way of providing a template, e.g.
> in the form of a pdb with CONECT records.
>
> Bill
>
> On 5/13/19 12:46 AM, Saikat Dutta chowdhury wrote:
>> Thank you for your reply.
>> I have used both pymol and vmd for viewing the molecule.
>>
>> with regards,
>> Saikat
>>
>> On Sun, May 12, 2019 at 2:23 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> On 5/11/19 11:40 PM, Saikat Dutta chowdhury wrote:
>>>> 1. When I am opening the pdb files for the system I found out that the
>>>> phosphate moieties are no longer attached to the amino acids.
>>> What viewer? Likely it's seeing a residue it doesn't know the bonding
>>> of, since it's an unknown res name.
>>>
>>> Bill
>>>
>>>
>>>
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Received on Mon May 13 2019 - 01:30:02 PDT
