{+ file: dna-rna_restraints.def directory: protocols +}
{+ description: Creates restraints to maintain conformation of DNA/RNA
Additions and changes were made to allow for flexibility during docking
Changes include:
flags to turn all options on or off
separation of sugar
pucker restraints and phosphate backbone restraints
option to have sugar-phosphate backbone dihedrals measured and restrained within a user defined error range
option to have the length of the Watson-Crick hydrogen bonds measured from the structure measured and restrained within a user defined error range.
+}
{+ comment:This file is to be read by refinement files that modify atom coordinates +}
{+ authors: Axel T. Brunger, and Paul D. Adams,
modified by Alexandre Bonvin and Marc van Dijk for HADDOCK use +}
set message=normal echo=on end
{- begin block parameter definition -} define(
{=========================================== base-pair planarity ===========================================}
{* Use planarity restraints for Watson-Crick base pairing *}
{+ choice: true false +}
{===>} basepair_planar=true;
{============================================== base planarity =============================================}
{* Restrain base planarity. This selection must only include nucleotide residues *}
{===>} bases_planar=((resid 1:45) and segid A);
{=================================== sugar-pucker dihedral angle restraints ================================}
{* Pick the dihedral angles of the sugar pucker from the input structure
and restrain them within the given error range *}
{+ choice: true false +}
{===>} dna_pick_pucdih=false;
{* residues with sugar pucker restrained - group 1 *}
{===>} pucker_1=(none);
{* conformation of group 1 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_1="a-form";
{* user defined sugar pucker for group 1 *}
{* dihedral C1'-C2'-C3'-C4' *}
{===>} dihedral_nu2_1=-34.9;
{* dihedral C1'-C2'-C3'-C4' error range *}
{===>} error_nu2_1=0.0;
{* dihedral C5'-C4'-C3'-C2' *}
{===>} dihedral_nu3_1=-86.4;
{* dihedral C5'-C4'-C3'-C2' error range *}
{===>} error_nu3_1=0.0;
{* dihedral C1'-O4'-C4'-C5' *}
{===>} dihedral_nu4_1=106.4;
{* dihedral C1'-O4'-C4'-C5' error range *}
{===>} error_nu4_1=0.0;
{* residues with sugar pucker restrained - group 2 *}
{===>} pucker_2=(none);
{* conformation of group 2 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_2="other";
{* user defined sugar pucker for group 2 *}
{* dihedral C1'-C2'-C3'-C4' *}
{===>} dihedral_nu2_2=-34.9;
{* dihedral C1'-C2'-C3'-C4' error range *}
{===>} error_nu2_2=0.0;
{* dihedral C5'-C4'-C3'-C2' *}
{===>} dihedral_nu3_2=-86.4;
{* dihedral C5'-C4'-C3'-C2' error range *}
{===>} error_nu3_2=0.0;
{* dihedral C1'-O4'-C4'-C5' *}
{===>} dihedral_nu4_2=106.4;
{* dihedral C1'-O4'-C4'-C5' error range *}
{===>} error_nu4_2=0.0;
{* residues with sugar pucker restrained - group 3 *}
{===>} pucker_3=(none);
{* conformation of group 3 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_3="other";
{* user defined sugar pucker for group 3 *}
{* dihedral C1'-C2'-C3'-C4' *}
{===>} dihedral_nu2_3=-34.9;
{* dihedral C1'-C2'-C3'-C4' error range *}
{===>} error_nu2_3=10.0;
{* dihedral C5'-C4'-C3'-C2' *}
{===>} dihedral_nu3_3=-86.4;
{* dihedral C5'-C4'-C3'-C2' error range *}
{===>} error_nu3_3=10.0;
{* dihedral C1'-O4'-C4'-C5' *}
{===>} dihedral_nu4_3=106.4;
{* dihedral C1'-O4'-C4'-C5' error range *}
{===>} error_nu4_3=10.0;
{* residues with sugar pucker restrained - group 4 *}
{===>} pucker_4=(none);
{* conformation of group 4 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_4="other";
{* user defined sugar pucker for group 4 *}
{* dihedral C1'-C2'-C3'-C4' *}
{===>} dihedral_nu2_4=-34.9;
{* dihedral C1'-C2'-C3'-C4' error range *}
{===>} error_nu2_4=10.0;
{* dihedral C5'-C4'-C3'-C2' *}
{===>} dihedral_nu3_4=-86.4;
{* dihedral C5'-C4'-C3'-C2' error range *}
{===>} error_nu3_4=10.0;
{* dihedral C1'-O4'-C4'-C5' *}
{===>} dihedral_nu4_4=106.4;
{* dihedral C1'-O4'-C4'-C5' error range *}
{===>} error_nu4_4=10.0;
{================================ phosphate backbone dihedral angle restraints =============================}
{* Pick the dihedral angles of the phosphate backbone from the input structure and
restrain them within the given error range *}
{+ choice: true false +}
{===>} dna_pick_bacdih=false;
{* residues with phosphate backbone restrained - group 1 *}
{===>} dihedral_1=(none);
{* conformation of group 1 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_1="a-form";
{* user defined sugar pucker for group 1 *}
{* alpha dihedral O3'-P-O5'-C5' *}
{===>} dihedral_alpha_1=-62.1;
{* alpha dihedral range *}
{===>} error_alpha_1=15;
{* beta dihedral P-O5'-C5'-C4' *}
{===>} dihedral_beta_1=-179.9;
{* beta dihedral range *}
{===>} error_beta_1=15;
{* gamma dihedral O5'-C5'-C4'-C3' *}
{===>} dihedral_gamma_1=47.4;
{* gamma dihedral range *}
{===>} error_gamma_1=15;
{* delta dihedral C5'-C4'-C3'-O3' *}
{===>} dihedral_delta_1=83.5;
{* delta dihedral range *}
{===>} error_delta_1=15;
{* epsilon dihedral C4'-C3'-O3'-P *}
{===>} dihedral_eps_1=-151.7;
{* epsilon dihedral range *}
{===>} error_eps_1=15;
{* zeta dihedral C3'-O3'-P-O5' *}
{===>} dihedral_zeta_1=-73.6;
{* zeta dihedral range *}
{===>} error_zeta_1=15;
{* residues with phosphate backbone restrained - group 2 *}
{===>} dihedral_2=(none);
{* conformation of group 2 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_2="other";
{* user defined sugar pucker for group 2 *}
{* alpha dihedral O3'-P-O5'-C5' *}
{===>} dihedral_alpha_2=-10.0;
{* alpha dihedral range *}
{===>} error_alpha_2=10.0;
{* beta dihedral P-O5'-C5'-C4' *}
{===>} dihedral_beta_2=136.4;
{* beta dihedral range *}
{===>} error_beta_2=40.0;
{* gamma dihedral O5'-C5'-C4'-C3' *}
{===>} dihedral_gamma_2=31.1;
{* gamma dihedral range *}
{===>} error_gamma_2=20.0;
{* delta dihedral C5'-C4'-C3'-O3' *}
{===>} dihedral_delta_2=-165.0;
{* delta dihedral range *}
{===>} error_delta_2=50.0;
{* epsilon dihedral C4'-C3'-O3'-P *}
{===>} dihedral_eps_2=-165.0;
{* epsilon dihedral range *}
{===>} error_eps_2=10.0;
{* zeta dihedral C3'-O3'-P-O5' *}
{===>} dihedral_zeta_2=-150.8;
{* zeta dihedral range *}
{===>} error_zeta_2=50.0;
{* residues with phosphate backbone restrained - group 3 *}
{===>} dihedral_3=(none);
{* conformation of group 3 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_3="other";
{* user defined sugar pucker for group 3 *}
{* alpha dihedral O3'-P-O5'-C5' *}
{===>} dihedral_alpha_3=-10.0;
{* alpha dihedral range *}
{===>} error_alpha_3=10.0;
{* beta dihedral P-O5'-C5'-C4' *}
{===>} dihedral_beta_3=136.4;
{* beta dihedral range *}
{===>} error_beta_3=40.0;
{* gamma dihedral O5'-C5'-C4'-C3' *}
{===>} dihedral_gamma_3=31.1;
{* gamma dihedral range *}
{===>} error_gamma_3=20.0;
{* delta dihedral C5'-C4'-C3'-O3' *}
{===>} dihedral_delta_3=-165.0;
{* delta dihedral range *}
{===>} error_delta_3=50.0;
{* epsilon dihedral C4'-C3'-O3'-P *}
{===>} dihedral_eps_3=-165.0;
{* epsilon dihedral range *}
{===>} error_eps_3=10.0;
{* zeta dihedral C3'-O3'-P-O5' *}
{===>} dihedral_zeta_3=-150.8;
{* zeta dihedral range *}
{===>} error_zeta_3=50.0;
{* residues with phosphate backbone restrained - group 4 *}
{===>} dihedral_4=(none);
{* conformation of group 4 *}
{+ choice: "a-form" "b-form" "other" +}
{===>} form_4="other";
{* user defined sugar pucker for group 4 *}
{* alpha dihedral O3'-P-O5'-C5' *}
{===>} dihedral_alpha_4=-10.0;
{* alpha dihedral range *}
{===>} error_alpha_4=10.0;
{* beta dihedral P-O5'-C5'-C4' *}
{===>} dihedral_beta_4=136.4;
{* beta dihedral range *}
{===>} error_beta_4=40.0;
{* gamma dihedral O5'-C5'-C4'-C3' *}
{===>} dihedral_gamma_4=31.1;
{* gamma dihedral range *}
{===>} error_gamma_4=20.0;
{* delta dihedral C5'-C4'-C3'-O3' *}
{===>} dihedral_delta_4=-165.0;
{* delta dihedral range *}
{===>} error_delta_4=50.0;
{* epsilon dihedral C4'-C3'-O3'-P *}
{===>} dihedral_eps_4=-165.0;
{* epsilon dihedral range *}
{===>} error_eps_4=10.0;
{* zeta dihedral C3'-O3'-P-O5' *}
{===>} dihedral_zeta_4=-150.8;
{* zeta dihedral range *}
{===>} error_zeta_4=50.0;
{============================================= C1'-C1' restraints ==========================================}
{* Have the length of the C1'-C1' virtual bonds measured and restraints. *}
{+ choice: true false +}
{===>} dna_pick_c1=false;
{* Error range used for C1'-C1' virtual bonds *}
{===>} c1_low=0.05;
{===>} c1_up=0.05;
{=========================================== Watson-Crick base pairs =======================================}
{* pick Watson-Crick restraint values from structure *}
{+ choice: true false +}
{===>} dna_pick_wc=false;
{* error range used for dna_pick_wc defined Watson-Crick restraints *}
{===>} wc_low=0.05;
{===>} wc_up=0.05;
{* for URI, for default much lower range... why?*}
{===>} wc_low_uri=0.01;
{===>} wc_up_uri=0.01;
{* residues which form Watson-Crick pairs *}
{* selection for pair 1 base A *}
{===>} base_a_1=(resid 1 and segid A);
{* selection for pair 1 base B *}
{===>} base_b_1=(resid 45 and segid A);
{* selection for pair 2 base A *}
{===>} base_a_2=(resid 2 and segid A);
{* selection for pair 2 base B *}
{===>} base_b_2=(resid 44 and segid A);
{* selection for pair 3 base A *}
{===>} base_a_2=(resid 3 and segid A);
{* selection for pair 3 base B *}
{===>} base_b_2=(resid 43 and segid A);
{* selection for pair 4 base A *}
{===>} base_a_4=(resid 4 and segid A);
{* selection for pair 4 base B *}
{===>} base_b_4=(resid 42 and segid A);
{* selection for pair 5 base A *}
{===>} base_a_5=(resid 5 and segid A);
{* selection for pair 5 base B *}
{===>} base_b_5=(resid 41 and segid A);
{* selection for pair 6 base A *}
{===>} base_a_6=(resid 6 and segid A);
{* selection for pair 6 base B *}
{===>} base_b_6=(resid 40 and segid A);
{* selection for pair 7 base A *}
{===>} base_a_7=(resid 7 and segid A);
{* selection for pair 7 base B *}
{===>} base_b_7=(resid 39 and segid A);
{* selection for pair 8 base A *}
{===>} base_a_8=(resid 9 and segid A);
{* selection for pair 8 base B *}
{===>} base_b_8=(resid 34 and segid A);
{* selection for pair 9 base A *}
{===>} base_a_9=(resid 10 and segid A);
{* selection for pair 9 base B *}
{===>} base_b_9=(resid 33 and segid A);
{* selection for pair 10 base A *}
{===>} base_a_10=(resid 11 and segid A);
{* selection for pair 10 base B *}
{===>} base_b_10=(resid 32 and segid A);
{* selection for pair 11 base A *}
{===>} base_a_11=(resid 12 and segid A);
{* selection for pair 11 base B *}
{===>} base_b_11=(resid 31 and segid A);
{* selection for pair 12 base A *}
{===>} base_a_12=(resid 13 and segid A);
{* selection for pair 12 base B *}
{===>} base_b_12=(resid 30 and segid A);
{* selection for pair 13 base A *}
{===>} base_a_13=(resid 14 and segid A);
{* selection for pair 13 base B *}
{===>} base_b_13=(resid 29 and segid A);
{* selection for pair 14 base A *}
{===>} base_a_14=(resid 15 and segid A);
{* selection for pair 14 base B *}
{===>} base_b_14=(resid 28 and segid A);
{* selection for pair 15 base A *}
{===>} base_a_15=(resid 16 and segid A);
{* selection for pair 15 base B *}
{===>} base_b_15=(resid 27 and segid A);
{* selection for pair 16 base A *}
{===>} base_a_16=(resid 17 and segid A);
{* selection for pair 16 base B *}
{===>} base_b_16=(resid 26 and segid A);
{* selection for pair 17 base A *}
{===>} base_a_17=(resid 18 and segid A);
{* selection for pair 17 base B *}
{===>} base_b_17=(resid 25 and segid A);
{* selection for pair 18 base A *}
{===>} base_a_18=(resid 19 and segid A);
{* selection for pair 18 base B *}
{===>} base_b_18=(resid 24 and segid A);
{* selection for pair 19 base A *}
{===>} base_a_19=;
{* selection for pair 19 base B *}
{===>} base_b_19=;
{* selection for pair 20 base A *}
{===>} base_a_20=;
{* selection for pair 20 base B *}
{===>} base_b_20=;
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Contact the webmaster for help, if required. Saturday, April 20, 2024 1:35:57 AM GMT
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