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

From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 17 Apr 2017 15:38:55 +0000

Thank you so much.

I have got confused then.


One more small question does it show any bond if I visualise it in chimera or anything? As after giving bond command I am unable to find any Hydrogen on Sulphur of CYS but chimera is not showing any bond.

Should I consider it to be bonded?

I am attaching screen shot for your reference.

________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Monday, April 17, 2017 4:14:58 AM
To: AMBER Mailing List
Subject: Re: [AMBER] coordinate bond between them and S and FE

Hi Thakur

I believe we are confusing things a bit.

You wrote before

"But bond command will form hydrogen bond, I want a coordinate bond"

I just asked where did you got that from, since the bond command CLEARLY makes what you call coordinate bonds, and I pointed you to the manual.
Adrian


On 4/17/17 10:45 AM, Thakur, Abhishek wrote:
> 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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--
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 - 09:00:02 PDT