Dear All,I want to restraint specific residue of my target protein through out simulation. In normal MD, first step of protein-ligand complex minimzation; water is free to move and gradually released restraint on both protein-ligand and counterions. After that, unrestraint minimization step water protein-ligand atoms and counterions set free to move. My question is, for my case can I apply restraint on above mentioned residues in unrestraint step of minimization and equilibration as well or not? I have pasted two unrestrain minimization step scripts below; suggest me which one is fine for my case.
unrestraint.in=============
protein-ligand md &cntrl
imin = 1,
maxcyc = 500,
ntpr = 5,
ntb = 1,
cut = 10.0
/
END
END
unrestraint.in===========protein-ligand md
&cntrl
imin = 1,
maxcyc = 500,
ntpr = 5,
ntb = 1,
ntr = 1,
cut = 10.0
/
Hold the system fixed
5.0
RES 268 532
END
END
Best Regards, Saman Yousuf Ali
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Received on Fri Sep 02 2016 - 01:00:02 PDT
