[AMBER] query regarding restraint on specific residues.

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Tue, 9 Aug 2016 07:00:57 +0000 (UTC)

Dear all,I have run MD using amber14 package, for a protein-ligand keeping the some part of protein rigid during whole simulation run.(Total residues of protein are 1-534, co-factor and ligand 535-538, counter ions 539-550 and  water molecules (TIP3P box) 551-19480). I wish to restraint 268-532 amino acids residues.

 However during unrestrained minimization step and unrestrained equilibration step I didn’t put restrain on the residues that I wished to restrain. Is it fine? or shall I apply restrain on the above mentioned residues (as I do not wish to analyze them) in every step of the simulation process? suggestions?
I will appreciate your help.
Thank you.
   Best Regards, Saman Yousuf AliJunior Research Fellow,
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Received on Tue Aug 09 2016 - 00:30:02 PDT
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