[gmx-users] Helical structure .itp file

[Justin Lemkul]

On 5/9/18 8:29 AM, rose rahmani wrote:
> Thank you somuch. I build it with anoyher software(Peptide buikder). But
> can i add NME and ACE terminals by GROMACS?

No. GROMACS has limited capacity to build anything. It can add H atoms 
and patch termini, but it has no ability to construct residues.

-Justin

> On Mon, 7 May 2018, 19:46 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 5/7/18 11:14 AM, rose rahmani wrote:
>>> Hi ,
>>>
>>> I want to build poly amino acids like poly threonine(ACE THR THR ... NME)
>>> BUT in its helical structure which its topology file is compatible with
>>> amber forcefield in GROMACS. Is there any way to build this structure in
>>> GROMACS?
>> GROMACS has no ability to construct molecules.
>>
>>> Would you please help me?
>> Use Leap in AMBER.
>>
>> -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

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