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

[Zheng Ruan]

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!

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
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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