AMBER Archive (2008)

Subject: AMBER: Minimisation and heating under GB conditions

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 03 2008 - 02:58:58 CST

Coming from experience with periodic boundary conditions, I started
minimization and heating of a large protein-polypeptide complex under
GB conditions, where I had no experience.Looking a posteriori to
tutorials, I wonder whether the conditions I used allow continuing
safely with MD.

minin:

mod21_polyp initial minimization prior to GB MD
&cntrl
 imin=1,
 maxcyc=5000,
 ncyc=2500,
 ntb=0,
 igb=1,
 cut=12
/

heating:

heating gradually under GB conditions
&cntrl
 imin=0, irest=0, ntx=1, ntb=0,
 igb=1, ntpr=500, ntwx=500,
 ntt=3, gamma_ln=2.0,
 nstlim=25000, dt=0.002,
 tempi=0.0, temp0=300.0,
 cut=12
/
 &wt TYPE='TEMP0', istep1=0, istep2=25000,
 value1=0.1, value2=300.0, /
 &wt TYPE='END' /

 I assumed that a cutoff of 12 would have been enough under GB
conditions but I am now unsure given the size of the protein (ca
20,000 atoms in total plus the polypeptide). Also, was the cost on no
SHAKE during heating worth while (and dt as large as 0.002 correct)?
Carrying out analysis by Ross Walker's script proceed_mdout.perl,
TEMP, EPTOT, EKTOT, and ETOT after heating are OK. Also, the initial
and "heated" structures superimpose at the open eye and Multialign in
Chimera is correct.

Thanks for advice

francesco pietra
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