Multiple topology and parameter file in run.cns

HADDOCK
1

I have a protein which I want to dock with a peptide, but the protein has N-Acetyl-Glucopyranose. I changes the residue name to GLP and I also have the parameters in glycans-uu.top and glycans-uu.param.

However, I should ideally modify the run.param or run.cns to include the parameters. However, when I try the following statements:

{===================== topology and parameter files ======================}

{* topology file for molecule 1 }
{===>} prot_top_mol1=“protein-allhdg5-4.top glycans-uu.top”;
{ topology file for molecule 2 *}
{===>} prot_top_mol2=“protein-allhdg5-4.top”;

OR

{===================== topology and parameter files ======================}

{* topology file for molecule 1 }
{===>} prot_top_mol1=“protein-allhdg5-4.top,glycans-uu.top”;
{ topology file for molecule 2 *}
{===>} prot_top_mol2=“protein-allhdg5-4.top”;

I get same error message, i.e. it cannot find the GLP residue in my system, however, GLP is present in glycans-uu.top and glycans-uu.param file. I cannot remove protein-allhdg5-4.top and protein-allhdg5-4.param as it contains parameters for proteins. However, it seems I cannot include multiple files topology files, though it seems including multiple topology files will solve the issue.

Hence, can anyone provide me a bit of assistance about this issue?

2

If you have the latest version of HADDOCK (2.4-July-2020) N-acetyl glucopyranose “should be” supported (no changes in topo/param files required in run.cns. The residue should however be properly named. The supported glucopyranose are:

  • NDG: 2-N-acetyl-alpha-D-glucopyranose
  • A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4
  • NAG: 2-N-acetyl-beta-D-glucopyranose
3

Hi,

Thank you so much for the suggestion.

However, replacing with NAG and including only the protein-allhdg5-4.top gives an error. The error is as follows:

%GENRES-ERR: residue NAG not found in topology files. Add topology definition.

Can you kindly let me know about the issue? Is it a feature available only in Haddock2.4-July2020? I am using its just previous version, Haddock2.4-June2020.

4

Yes you do need the July version as I explained.

Send me an email