Would someone teach me how to use ibelly option under restraint atoms?
I ran job bellow, but I found error message in
Fr-Rh_Ph-Est_-20_-20_vac-12.out file. It said "Could not find cntrl
namelist".
$AMBERHOME/exe/sander -O -i Free-min-ibelly.in -o
Fr-Rh_Ph-Est_-20_-20_vac-12.out -p Fr-Rh_Ph-Est_-20_-20_vac.prmtop -c
Fr-Rh_Ph-Est_-20_-20_vac.inpcrd -r Fr-Rh_Ph-Est_-20_-20_vac.rst -ref
Fr-Rh_Ph-Est_-20_-20_vac.inpcrd
Free-min-ibelly.in
---------------------------------------------------------------
Minimization with Cartesian restraints
&cntrl
imin=1,
maxcyc=40000,
ncyc=30,
ntmin=1,
ntpr=5,
ibelly=1,
ntrx=1,
restraint_wt=5000,
bellymask='.1-16,18,20-23,27-51',
ntb=0,
cut=12.0,
/
---------------------------------------------------------------
I suspect the usage of bellymask. Are there any other wrong descriptions?
Thanking you in advance.
Akihiro Yamane
Ex-professor of Mie chukyo university junior college(Closed in 2012)
e-mail:yamane_929.nifty.com
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Received on Mon Dec 15 2014 - 04:30:02 PST
