Would someone let me know how to restrain atoms during optimization?
I want to depict Ramachandran plot of disaccharide in vacuum under fixing
atoms condition.
I let Amber run a job bellow.
$AMBERHOME/exe/sander -O -i Free_min.in -o Rha_vac.out -p Rha_vac.prmtop -c
Rha_vac.inpcrd -r Rha_vac.rst -ref Rha_vac.inpcrd
Free_min.in
---------------------------------------------------------------
Minimization with Cartesian restraints
&cntrl
imin=1,
maxcyc=40000,
ncyc=20000,
ntmin=1,
ntpr=5,
ntr=1,
ntrx=1,
restraint_wt=5000,
restraintmask='.17,19,24,25,26',
ntb=0,
cut=12.0,
/
---------------------------------------------------------------
>From the result, fixed atoms moved slightly, dihedral angel(atom
26-25-24-19) changed from -20.0 to -19.8 and one(atom 25-24-19-17) from
-20.0 to -20.4, bond angle(atom 25-24-19) from 110.8 to 110.9.
Rha_vac.out gives Final Results and Energy converged.
I know using higher restraint_wt values (10000, for example) gives less
movement of atoms but I am afraid using higher restraint_wt value might give
insufficient opimization.
Is my job appropriate?
Best wishes
------------------------------------------------
Akihiro Yamane
Mie Chukyo University Junior College(College was closed )
1846 Kubocho Matsusaka Mie Japan
e-mail:yamane_929.nifty.com
-----------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 25 2014 - 22:30:02 PST
