Re: [AMBER] coordinate bond between them and S and FE

From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 17 Apr 2017 14:45:31 +0000

Hi Dr.Adian


I am sure it a coordinate bond as it is between Fe of HEME and S of CYS. I am attaching a screen shot of my system for your reference


Will this bond command make coordinate bonds?


With regards,

-AT


________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Friday, April 14, 2017 9:48:37 AM
To: AMBER Mailing List
Subject: Re: [AMBER] coordinate bond between them and S and FE

why do you say that ?


 From the amber16 manual:


13.5.9. bond

bond atom1 atom2 [ order ]

Create a bond between atom1 and atom2. Both of these ATOMs must be
contained by the same UNIT. By
default, the bond will be a single bond. By specifying “-”, “=”, “#”, or
“:” as the optional argument, order, the
user can specify a single, double, triple, or aromatic bond,
respectively. Example:

bond trx.32.SG trx.35.SG




On 4/14/17 4:44 PM, Thakur, Abhishek wrote:
> But bond command will form hydrogen bond, I want a coordinate bond
>
> Sent using OWA for iPhone
> ________________________________
> From: Marcos Serrou do Amaral <marcossamaral.gmail.com>
> Sent: Friday, April 14, 2017 8:24:54 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] coordinate bond between them and S and FE
>
> On Fri, Apr 14, 2017 at 3:18 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
>> Can you suggest me how to tell tleap to make it a coordinate bond. I am
>> afraid as by giving a bond command it will form hydrogen bond with it.
>>
> You need to use 'bond' command between S and a carbon atom. If your S atom
> has a hydrogen atom, you need to throw it away. I am not sure, but I think
> it is possible to do it in leap.
>
> Good luck!
> ---
> Marcos S.A.
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Apr 17 2017 - 08:00:03 PDT