Yes I have got it by printbonds commands
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, April 20, 2017 8:17:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make sure there is bond in my complex
I guess "bond" command. But please try playing with "help" in
interactive command first. It's much easier to "see" it.
Hai
On Thu, Apr 20, 2017 at 3:06 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> 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 - 12:30:04 PDT
