AMBER Archive (2005)

Subject: AMBER: fixing protein for minimisation of solvent

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Sat Sep 03 2005 - 05:56:55 CDT

Dear Amber users,
 
As part of my minimisation protocol I am trying to first minmise the solvent whilst keeping the protein fixed. My input file is as follows;
 
isol dIII min - solv min
 &cntrl
    imin=1, maxcyc=500,
    cut=14.0,
    ntb=1,
    ntpr=10,
    ntr=1,
    restraint_wt=1.0,
    restraintmask= :1-174,
 &end

Is this the correct method for doing this and what value for the restraint_wt would be appropriate to ensure that the protein will remain fixed? Your help on this would be much appreciated.
 
Many thanks in advance
 
simon whitehead
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