Re: [AMBER] Manually set residues Protonation states for HIS and CYS

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From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Sun, 17 Sep 2017 15:30:16 -0400

here is the system that I want to prepare for MD simulation.

Thanks

On Sun, Sep 17, 2017 at 3:27 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:

> Hi everybody
>
> If our protein's ligand have carboxylate-mediated interactions with the
> conserved YxSxR motif of protein as well as hydrophobic interactions,
> should we change the residues name like HIS to HID because it does not have
> bond with ligand. and CYS remain same according to our scenario.
>
> kindly guide if i am wrong.
>
> Regards
>
>

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chemical/x-pdb attachment: 4iae.pdb

Received on Sun Sep 17 2017 - 13:00:02 PDT