[gmx-users] AMP_itp

[Justin Lemkul]

On 6/13/18 11:11 AM, niki24 at tezu.ernet.in wrote:
>> On 5/31/18 10:54 AM, niki24 at tezu.ernet.in wrote:
>>> Hello,
>>>
>>> Can anyone provide me with the correct topolgy file for
>>> Adenosine-5'-Monophosphate(AMP).
>> AMP is part of the CHARMM36 force field. Generate the topology with
>> pdb2gmx.
>>
>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>>
>> -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
>>
>> ==================================================
>>
>>
>>
>> ------------------------------
>> Dear Justin,
> Thanks a lot for your reply.
> I have generated the topology using CHARMM36 forcefield.
> But, however i would like to convert it into an itp file to
> be used in gromos54a7 force field.
>
> I am not being able to properly generate the itp file.
>
> I have attached the topol.top file generated for AMP through CHARMM36 in
> the link provided.
>
> https://www.dropbox.com/s/uetrnnim4a30j01/topol.top?dl=0

You can't convert one force field to another. Force fields are 
self-consistent entities. You have to choose one force field and stick 
to it. If GROMOS96 doesn't meet your needs, then use a force field that 
does, like CHARMM36.

-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

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