[Question from NMRWiki Q&A forum] How to set up RAMA database restraints for NIH-XPLOR (for peptide NMR structure calcu

[nmrlearner]

How to set up RAMA database restraints for NIH-XPLOR (for peptide NMR structure calculation)?

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... Thanks.

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

!(1) initial setupevaluate ($krama = 1.0) !intraresidue proteinevaluate ($kramalr = 0.15) !long range proteinevaluate ($kvirt1doverall=0.0001) !virtual ca-caevaluate ($kvirt1d=0.001)evaluate ($kvirt2d=0.001)evaluate ($kvirt3d=0.001)evaluate ($knuc = 1.000) !nucleic acidsrama nres=10000 !set message off echo off end @QUARTS:2D_quarts_new.tbl @QUARTS:3D_quarts_new.tbl @QUARTS:4D_quarts_intra_new.tbl @QUARTS:forces_torsion_prot_quarts_intra.tbl !intraresidue protein torsion angles @GAUSSIANS:shortrange_gaussians.tbl @GAUSSIANS:new_shortrange_force.tbl @GAUSSIANS:longrange_gaussians.tbl @GAUSSIANS:longrange_4D_hstgp_force.tbl @GAUSSIANS:virtualTA_hstgp_gauss.tbl @GAUSSIANS:virtualTA_force_hstgp.tblend....!(2) before cooling loopevaluate ($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

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