Thank you for your suggestion.
After loading the prmtop I am able to visualize the proper connectivity.
With regards,
Saikat
On Mon, May 13, 2019 at 1:36 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
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Received on Mon May 13 2019 - 04:00:03 PDT
