[AMBER] How to restrain atoms

From: Akihiro Yamane <yamane_929.nifty.com>
Date: Wed, 26 Nov 2014 15:03:13 +0900

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

-----------------------------------------------------

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Received on Tue Nov 25 2014 - 22:30:02 PST
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