[AMBER] Residue Protonation State

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Sat, 2 Dec 2017 14:07:50 +0500

Dear Amber Users

Can protonation state of cys residue affect the system. I forget to change
the CYM -vely charge to CYS neutral while this residue not connected to any
metal (system does not have metal attached with this cys). Is it essential
to replace the residue to cys in the above mention system or I can continue
the simulation for next heat step.
 Kindly also guide if some part of protein (domain) during minimization or
production MD convert to loop what its mean.

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Received on Sat Dec 02 2017 - 01:30:02 PST
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