Discussion group for the ARIA software

[Torres Félix <felix.torres AT phys.chem.ethz.ch>]

Dear all,

I would like to update my question. I could figure out that some path was picking the wrong topology file.

Nevertheless, I still struggle with the parameter file.

I could introduce quite easily the bond, angle and nonbonded parameters. However, I still have an error for the improper parameters, even if I included them in the parallhdg5.4.pro.

Any idea?

Best regards,

Felix

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Félix Torres (PharmD, PhD student)

ETH Zürich

BioNMR group (Prof Riek)

Vladimir-Prelog Weg 2, 8093, Zurich

+41 44 633 44 05

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De : aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> de la part de Torres Félix <felix.torres AT phys.chem.ethz.ch>
Envoyé : mardi 5 janvier 2021 14:56:59
À : aria-discuss AT services.cnrs.fr
Objet : [aria-discuss] CNS ligand topology missing

 

Dear all,

I am trying to refine in water a CYANA calculated protein-ligand structure. 

For this I would need to generate a protein-ligand complex.pdb and complex.mtf files.

Therefore, I generated the ligand topologies (.top) and parameters (.param) with LigParGen.

I added the topologies at the end of topallhdg5.4.pro, and the parameters at the end of parallhg5.4.pro.

Of course, I took care of defining the name of my residue (residue JO2) prior to the topology entries, and I close it with a "end" command. Exactly the same as for the other residues that were already in the file.

Then, I use the Recoord scripts, and I run generate.sh. 

However, the ERROR_generate tells me that the residue JO2 is not defined. When I open the generate.out I do not  see the lines for the topologies of my new residue.

Does anybody have experience with the generation of CNS compatible protein-ligand structures?

Best regards,

Felix

------------------------------------------------------------

Félix Torres (PharmD, PhD student)

ETH Zürich

BioNMR group (Prof Riek)

Vladimir-Prelog Weg 2, 8093, Zurich

+41 44 633 44 05

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