Hi Yi An,
Just to have an idea how is looking default restraint function (IALTD=0)
and which is the meaning of parameters r1,r2,r3,r4,
check this figure:
http://www.google.cz/imgres?q=%22well+with+a+square+bottom%22&hl=cs&client=badoo&sa=X&biw=1920&bih=944&tbm=isch&prmd=imvns&tbnid=9TZNFCqvPAWviM:&imgrefurl=http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm&docid=w82wgOEgQ0fQKM&imgurl=
http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/dna_NMR/energy_penalty.gif&w=410&h=210&ei=lJmZUNKcFM_O4QT_lIG4BA&zoom=1&iact=hc&vpx=1206&vpy=165&dur=41&hovh=161&hovw=314&tx=142&ty=111&sig=113383803473922675655&page=1&tbnh=132&tbnw=270&start=0&ndsp=65&ved=1t:429,r:7,s:0,i:90
maybe that in that tutorial you could find also many useful information
(not sure if some of that are not too obsolete).
Here is simple example for restraint file named e.g. RST.txt :
-----------------------RST.txt--------------------------------------------------------
# r_aA :
&rst
ixpk= 0, nxpk= 0, iat= 1, 4948, r1=11.622892 , r2= 16.622892, r3=
16.622892, r4=21.622892,
rk2=50.0, rk3=50.0,
&end
# THETA_A :
&rst
ixpk= 0, nxpk= 0, iat= 5, 1, 4948, r1=34.160172, r2= 64.160172, r3=
64.160172, r4=94.160172,
rk2=150.0, rk3=150.0,
&end
# FI_A :
&rst
ixpk= 0, nxpk= 0, iat= 14, 5, 1, 4948, r1=-179.297707, r2= -149.297707,
r3= -149.297707, r4=-119.297707,
rk2=150.0, rk3=150.0,
&end
--------------------------------------------------------------------------------------
In the first record ( # r_aA : )there is defined distance restraint
between atoms 1 and 4948, equilibrium distance is here 16.622892 A. The
potential is harmonic for atom distance between r1 and r4 (because r2=r3)
and linear outside this interval. So the harmonic potential between r1 and
r4 seems in this case like 50.0*( R - 16.622892)^2 , Left side linear
extension has slope 2*50.0*( 11.622892 - 16.622892 ) = -500 and right side
linear extension has slope 2*50.0*( 21.622892 - 16.622892 ) = 500
In the second record (# THETA_A :) you have similarily defined angle
restraint. Angle is defined by 3 atoms with atom numbers 5, 1, 4948. Again
we have here the same type of potential as in the first case e.g. harmonic
between the angles 34.160172 and 94.160172 degrees with
equilibrium value in 64.160172 with force constant 150.0 so it is 150.0*(
theta - 64.160172)^2 . Outside the <r1, r4> we have again linear
extensions.
In the third case we have defined restraint of the torsion angle defined
by the atoms number 14,5,1,4948 the meaning of all the constants is the
same as in the two previous cases.
'#' means comment
Perhaps there is also some alternative, more "user friendly" way to define
restraints (see the recommended section in Amber manual), but I am using
this old and for me fine way.
In the given input file (*.in) you have to put information about the text
file, where the restraints are defined (in our case file RST.txt). Use
variable DISANG for this purpose, like here in this sample *.in file.
----------------------------------
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 10000, ntwr = 100000, ntwx = 10000,
ntf = 2, ntc = 2,
ntb = 2, cut = 10,
nstlim = 100000, dt = 0.002,
temp0 = 298.0, ntt = 3, gamma_ln = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
nmropt=1,
&end
&wt type='END' /
LISTOUT=POUT
DISANG=RST.txt
----------------------------------
Let's notice nmropt > 0. LISTOUT=POUT means that the dviations of the
restrained quanities will be writen in the *.out file.
Best,
Marek
Dne Tue, 06 Nov 2012 20:53:22 +0100 <anyiphysics.gmail.com> napsal/-a:
> Hi all,
>
> I'm now trying to apply angle restraint to a ligand in my system. I read
> the Amber11 manual buy got confused. It seems that we can only apply
> restraint to torsional angles using makeANG_RST. If anyone knows how to
> restrain an angle between three atoms (not dihedral angle) please teach
> me.
> Thank you very much.
>
> Yi An
> Graduate Student
> Department of Chemistry
> Texas A&M University
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Received on Tue Nov 06 2012 - 16:30:02 PST
