[gmx-users] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Thanks for your comment and sorry for my weird english. I must have been in my thoughts :).

I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a suggestion how setup a system like this?

Thanks,
Max


> On May 21, 2015, at 4:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 5/21/15 4:30 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice?
>> 
> 
> Sounds reasonable.
> 
> -Justin
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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