Re: [AMBER] Is there a trick to fix a poor structural feature?

From: <tec3.utah.edu>
Date: Wed, 24 Apr 2013 20:51:23 -0600 (MDT)

> 2. the first step of the MD gives ***** even if I start the temp at 0 and
> raise it to 3K with dt=0.00001, and shake off and
>
> I will keep minimizing...

What I often suggest is to try minimizing first with electrostatics turned
off; this often fixes clashes (although this will not recover from ring
fusions, e.g. when a chain and a ring overlap, miminimization can put the
chain the in middle of a ring).

min_noelec.in (w/out water):

production
 &cntrl
    imin = 1, maxcyc = 25000, ncyc = 25000,
    ntb = 0,
    cut = 9.0,
    nmropt = 1, ntpr = 500,
 &end
 &wt
   type = 'ELEC', value1 = 0.0,
 &end
 &wt
   type = 'END',
 &end
 &rst
   iat = 0,
 &end

--tec3



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Received on Wed Apr 24 2013 - 20:00:23 PDT
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