Thank you very much, Marek!
On , Marek Maly <marek.maly.ujep.cz> wrote:
> 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 eg 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 eg 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 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 - 17:00:03 PST
