[gmx-users] atom types of hydrogens
jalemkul at vt.edu
Thu Apr 11 17:14:13 CEST 2019
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 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
> 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 A. Lemkul, Ph.D.
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
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