[gmx-users] situation where ligand is connected to amino acid

[Justin Lemkul]

On 1/2/18 9:40 PM, Zheng Ruan wrote:
> Hi Ming and Justin,
>
> I have the same situation in which my protein has a cysteine residue
> covalently linked to a drug. I'm regularly using amber99sb-ildn force
> field. Is there existing tools that can help parameterize the modified
> residue? Thank you!

Sure, antechamber, RED (PyRED) server, etc.

-Justin

> Ruan
>
> On Tue, Jan 2, 2018 at 8:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/2/18 2:59 PM, MD wrote:
>>
>>> Hi Gromacs folks,
>>>
>>> I want to simulation a protein complexed with a ligand. However, the
>>> protein covalently bonded with the ligand via N-C bond. The ligand has a
>>> size of 27 atoms. The solution I could think of now is to create a
>>> modified
>>> amino acid which includes both the amino acid side chain and the connected
>>> ligand in rtp and make modifications in ffbonded.itp accordingly.
>>>
>>> I wonder if there is another route to get this done?
>>>
>> Your approach is correct.
>>
>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
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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.biochem.vt.edu/people/faculty/JustinLemkul.html

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