Hi Hai
Do you mean something like hydrogen bond analysis ?
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, April 20, 2017 7:59:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make sure there is bond in my complex
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 - 12:30:03 PDT
