[gmx-users] Problem in protein ligand interaction

[Du, Yu]

Hi Cristina, 

Previous ultra-long conventional molecular dynamics works have shown that ligand can find its binding pocket and finally bind in a crystal complex pose. Also enhance sampling techniques, e.g. metadynamics, can speeed the binding process. 

So, if you want ligand to find its binding pocket, you may need long-time simulation or enhance sampling. 

Distance restraint on the ligand is harmonic force, it indeed can affect the interaction between ligand and protein.

> -----原始邮件-----
> 发件人: "Gonzalez Fernandez, Cristina" <cristina.gonzalezfdez at unican.es>
> 发送时间: 2020-03-20 17:59:05 (星期五)
> 收件人: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> 抄送: 
> 主题: [gmx-users] Problem in protein ligand interaction
> 
> Dear Gromacs users,
> 
> 
> I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid in the opposite direction. How could I achieve that the lipid reaches the protein binding site? Could I include some distance restraints that help the lipid to move to the binding pocket and then switch them off or this idea would lead to unreliabe results?
> 
> 
> Thank you in advance for all your help!
> 
> 
> Regards,
> 
> 
> Cristina
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275