My software notes

February 22, 2012

Things must be changed before Protein-RNA docking using Haddock

Filed under: xplor/xplor-nih/cns — kpwu @ 8:10 pm
Tags: , ,

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

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