Hi, you can use cpptraj or ParmED interactive mode to print out the
bond information. Use "help" or manual for info.
Hai
On Thu, Apr 20, 2017 at 2:56 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi everyone,
>
>
> I have made a complex with tleap.
>
> In that complex I have made 6 bonds using bond command.
>
> But when I visualize that in chimera I am unable to find any bonds.
>
> So then I have used my prmtop and inpcrd file and cpptraj to generate pdb file for me to make sure there is a bond. But not I can see one of the bonds, remaining 5 bonds are not shown by chimera till now.
>
> Then I have visualized in VMD and I can find 5 bonds but still 1 bond is missing.
>
>
> Can anyone suggest me a way by which I can make sure that my parameter files have bonds.
>
>
>
>
> with regards,
>
> -Abhi
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Received on Thu Apr 20 2017 - 12:00:03 PDT
