[gmx-users] interaction between ligand and protein

[Mahboobeh Eslami]

I sincerely thank you for your answer.
 Is the RMSD values of  system be monitored or the RMSD values of only protein or ligand. Which RMSD do I check? 

     On Sunday, November 30, 2014 8:34 PM, Onur Tuna <onurtuna at hacettepe.edu.tr> wrote:
   

 Dear Mahboobeh,

You mean from which frame you should choose? If so, first look at RMSD values in order to make sure your system is stable. If it is stable you can choose the last configuration.

Best,
Onur

> On 30 Nov 2014, at 18:57, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
>
>  hi GMX users
>
> i have simulated the protein-ligand complex by gromacs for 20ns. Which configuration should be chosen for the study of interactions between proteins and ligands?
>
> Thank you for your kindness
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The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission.