[AMBER] Optimization under restraint atoms using ibelly option

From: Akihiro Yamane <yamane_929.nifty.com>
Date: Mon, 15 Dec 2014 21:12:08 +0900

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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 15 2014 - 04:30:02 PST
Custom Search