[gmx-users] GTP

[Justin Lemkul]

On 8/15/18 9:08 AM, Mahdi Sobati Nezhad wrote:
> Excuse me I don't understand completely, I residue I see Gua and Ade. You
> say I change Gua base with Ade base in the ATPs residue?!
> What about my hydrogen bonds?!
> Do my charges don't change?!

Additive force fields are constructed from building blocks. Look at the 
normal library of nucleosides and nucleotides in the force field. The 
sugar and phosphate parameters don't change as a function of the 
nucleobase. Just swap G for A in ATP and you will have GTP.

-Justin

> Thanks for your help
>
> On Wed, 15 Aug 2018 16:00 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote:
>>> hello
>>> I'm working on a protein that contains GTP in its structure. I can't find
>>> any force field that contains GTP's residue but I find a force field that
>>> contains the ATPs residue! There is any way that I can convert ATP to
>> GTP?!
>>> Or any other idea?!
>> Just replace the Ade base with Gua.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================