Just a note for RNA-protein docking using Haddock 2.1
System: Mac OS 10.6.8, CNS 1.3, Haddock 2.1
1. RNA (or DNA) nomenclature in CNS is not same as the names in PDB.
e.g. ACU in PDB = ADE CYT URI in CNS
The “nucleic acid builder” developed in David Case group can generate template structure 100% satisfied to CNS format
2. change all paramenters/toppar file from version 5.3 to 5.4 (if using Mac/CNS 1.3)
3. Assume molecule B is RNA/DNA, then in
A. “filenames”, change {===>} dna_B=false; to {===>} dna_B=true (for DNA);
B. “DNA-RNA restraints”, change {===>} dnarest_on=false; to {===>} dnarest_on=true;
also copy file “dna-rna_restraints.def” to run1/data/sequence (if it’s run1 in your path)
The “dan-rna_restraints.def” can be found in the Haddock example folder — see 3cro
–> change the resid numbers at lines 30, 35
=== example ===
{========================== base planarity ===========================}
{* Nucleic acid residues to have base planarity restrained. This selection
must only include nucleotide residues *}
{===>} bases_planar=(resid 1:11 and segid B);
{========================== sugar puckers ============================}
{* residues with sugar pucker restrained – group 1 *}
{===>} pucker_1=(resid 1:11 and segid B);
==============
C. “topology and parameter files”, change
C1. prot_top_B=”topallhdg5.4.pro” to prot_top_B=”dna-rna-allatom-hj-opls-1.3.top“
C2. prot_link_B=”topallhdg5.4.pep to to prot_link_B=”dna-rna-1.3.link“
C3. prot_par_B=”parallhdg5.4.pro” to prot_par_B=”dna-rna-allatom-hj-opls-1.3.param“
