[gmx-users] atom types of hydrogens

[Justin Lemkul]

On 4/10/19 4:12 AM, boshra.moradi.61 wrote:
>
> در 2019-04-09 20:08، Justin Lemkul نوشته است:
>
>>
>>
>> On 4/9/19 11:26 AM, boshra.moradi.61 wrote:
>>>   Dear all,
>>>
>>> i'm new om gromacs and my molecule is D-glucosamine.i introduced it via
>>> inserting in aminoacids.rtp file.my question is how nominate four
>>> H-atoms . i want atomtypes.atp to find the atometype of these four atoms
>>> but i didn't find.i want you to guide me about this problem,could you
>>>
>>
>> Most force fields should already have parameters for such a species. 
>> In any case, the information in the .atp file is likely inadequate 
>> but you can make the assignments based on the same moieties in 
>> residues defined within the .rtp file.
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>
> Dear Justin,
>
> Can you clarify this sentence for me, i don't understand what do you 
> mean by "  you can make the assignments based on the same moieties in 
> residues defined within the .rtp file."
>
> i search .rtp file and i can't find the type of these four hydrogen.in 
> addition, the force field is : opls-aa .
>

You have aliphatic, hydroxyl, and amino hydrogens. Their types can be 
assigned from similar groups. Search the literature to see if there are 
specific parameters for carbohydrates in OPLS-AA. I know there are for 
AMBER and CHARMM.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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