Hello, has anyone managed to set up RAMA restraints for NIH-XPLOR? For some reason I'm always getting E(RAMA)=0.000 in the output, that is the term is registered, but the the energy is always zero.

Somehow either parameters for the interaction are assumed to be zero or there are no atoms that have those energy term.

In my sa.inp I've got the following setup:

!(1) initial setup
evaluate ($krama = 1.0)    !intraresidue protein
evaluate ($kramalr = 0.15) !long range protein
evaluate ($kvirt1doverall=0.0001) !virtual ca-ca
evaluate ($kvirt1d=0.001)
evaluate ($kvirt2d=0.001)
evaluate ($kvirt3d=0.001)
evaluate ($knuc = 1.000)    !nucleic acids

rama
    nres=10000
    !set message off echo off end

    @QUARTS:2D_quarts_new.tbl
    @QUARTS:3D_quarts_new.tbl
    @QUARTS:4D_quarts_intra_new.tbl
    @QUARTS:forces_torsion_prot_quarts_intra.tbl


    !intraresidue protein torsion angles
    @GAUSSIANS:shortrange_gaussians.tbl
    @GAUSSIANS:new_shortrange_force.tbl

    @GAUSSIANS:longrange_gaussians.tbl
    @GAUSSIANS:longrange_4D_hstgp_force.tbl

    @GAUSSIANS:virtualTA_hstgp_gauss.tbl
    @GAUSSIANS:virtualTA_force_hstgp.tbl
end
....
!(2) before cooling loop
evaluate ($ini_rama = 0.002)        evaluate ($fin_rama = 1.0)
evaluate ($rama_fac = ($fin_rama/$ini_rama)^(1/$ncycle))
evaluate ($krama = $ini_rama)
evaluate ($ini_lr = 0.0002)        evaluate ($fin_lr = 0.15)
evaluate ($lr_fac = ($fin_lr/$ini_lr)^(1/$ncycle))
evaluate ($kramalr = $ini_lr)
evaluate ($ini_nuc = 1.000)        evaluate ($fin_nuc = 2.0)
evaluate ($nuc_fac = ($fin_nuc/$ini_nuc)^(1/$ncycle))
evaluate ($knuc = $ini_nuc)

evaluate ($kvirt1d=$kramalr)
evaluate ($kvirt2d=$kramalr)
evaluate ($kvirt3d=$kramalr)

!(3) inside cooling loop
    evaluate ($krama  = $krama*$rama_fac)
    evaluate ($kramalr  = $kramalr*$lr_fac)
    evaluate ($knuc  = $knuc*$nuc_fac)
    evaluate ($kvirt1d=$kramalr)
    evaluate ($kvirt2d=$kramalr)
    evaluate ($kvirt3d=$kramalr)

    parameter  nbonds repel=$radius   end end
    constraints interaction (not name SG) (all)
                 weights * 1. rama $krama vdw $k_vdw end end

Hello, has anyone managed to set up RAMA restraints for NIH-XPLOR? For some reason I'm always getting E(RAMA)=0.000 in the output, that is the term is registered, but the the energy is always zero.

Somehow either parameters for the interaction are assumed to be zero or there are no atoms that have those energy term.term... Thanks.

In my sa.inp I've got the following setup:

!(1) initial setup
evaluate ($krama = 1.0)    !intraresidue protein
evaluate ($kramalr = 0.15) !long range protein
evaluate ($kvirt1doverall=0.0001) !virtual ca-ca
evaluate ($kvirt1d=0.001)
evaluate ($kvirt2d=0.001)
evaluate ($kvirt3d=0.001)
evaluate ($knuc = 1.000)    !nucleic acids

rama
    nres=10000
    !set message off echo off end

    @QUARTS:2D_quarts_new.tbl
    @QUARTS:3D_quarts_new.tbl
    @QUARTS:4D_quarts_intra_new.tbl
    @QUARTS:forces_torsion_prot_quarts_intra.tbl


    !intraresidue protein torsion angles
    @GAUSSIANS:shortrange_gaussians.tbl
    @GAUSSIANS:new_shortrange_force.tbl

    @GAUSSIANS:longrange_gaussians.tbl
    @GAUSSIANS:longrange_4D_hstgp_force.tbl

    @GAUSSIANS:virtualTA_hstgp_gauss.tbl
    @GAUSSIANS:virtualTA_force_hstgp.tbl
end
....
!(2) before cooling loop
evaluate ($ini_rama = 0.002)        evaluate ($fin_rama = 1.0)
evaluate ($rama_fac = ($fin_rama/$ini_rama)^(1/$ncycle))
evaluate ($krama = $ini_rama)
evaluate ($ini_lr = 0.0002)        evaluate ($fin_lr = 0.15)
evaluate ($lr_fac = ($fin_lr/$ini_lr)^(1/$ncycle))
evaluate ($kramalr = $ini_lr)
evaluate ($ini_nuc = 1.000)        evaluate ($fin_nuc = 2.0)
evaluate ($nuc_fac = ($fin_nuc/$ini_nuc)^(1/$ncycle))
evaluate ($knuc = $ini_nuc)

evaluate ($kvirt1d=$kramalr)
evaluate ($kvirt2d=$kramalr)
evaluate ($kvirt3d=$kramalr)

!(3) inside cooling loop
    evaluate ($krama  = $krama*$rama_fac)
    evaluate ($kramalr  = $kramalr*$lr_fac)
    evaluate ($knuc  = $knuc*$nuc_fac)
    evaluate ($kvirt1d=$kramalr)
    evaluate ($kvirt2d=$kramalr)
    evaluate ($kvirt3d=$kramalr)

    parameter  nbonds repel=$radius   end end
    constraints interaction (not name SG) (all)
                 weights * 1. rama $krama vdw $k_vdw end end