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Alexander Pushkarchuk

z-matrix of Polyacrylamide monomer

Dear The Polymer Modeler developers! I build the z-matrix of Polyacrylamide monomer which is give below. But in process of simulation of structure of polymer I get bad structure. Maybe I was wrong in the construction of a z-matrix? Could you help me?

4 # Number of backbone atoms H_ C_3 1 00001.9291 C_3 1 00001.1002 2 00042.9035 H_ 2 00001.1044 1 00108.6082 3 00110.2305 C_2 2 00001.5128 1 00138.8045 3 00323.9256 H_ 3 00001.1034 1 00101.9051 2 00121.7836 H_ 3 00001.1038 1 00100.9475 2 00240.5443 O_2 5 00001.3922 2 00120.2354 4 00162.6206 N_2 5 00001.4066 2 00120.7279 4 00341.9055 H_ 9 00001.0186 5 00121.6204 8 00160.5530 H_ 9 00001.0184 5 00121.4820 8 00019.2207 H_ 2 00001.0948 1 00082.5059 3 00216.2973

Thank you! Alexander

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    Magnus Bergh

    Dear Nanohub, I have basically the same problem; I have xyz-coorditaes of a monomer, and want to convert to the z-matrix format that Polymer Modeler uses. The Gaussian gzmat format in iBalel doesn’t really look like the Polymer Modeler. What is the best way of generating the proper z-mat format with Dreiding FF format for elements etc.? Thanks, Magnus, Sweden

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      Benjamin P Haley

      Please see the comments on this ticket: https://nanohub.org/support/ticket/259670

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        Benjamin P Haley

        Here are the comments from the ticket referenced above: The Fenske-Hall Z-Matrix format supported by OpenBabel is compatible with the zmatrix format used by PolymerModeler. Use -ofh with the command line babel tool to produce an output file in this format. The elements in column 1 of the zmatrix need to be converted to Dreiding format (e.g. “H” to “H_”, “O” to “O_2”, “C” to “C_2”, “C_3”, or “C_R”). This would need to be done by hand. We’re working on new modules for this tool to allow PDB and Gaussian z-matrix inputs, as well as auto-typing atoms based on their connectivities.

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    Benjamin P Haley

    Hi, Sorry for the delay in replying. The z-matrix needs some work, I think. The backbone bond between the first two C atoms (atoms 2 and 3) is not explicitly specified in the z-matrix. The builder will identify this missing bond (I checked — it does find the missing bond) but the process of rotating torsions to find a good configuration relies on the bonds

    in the z-matrix. In other words, the torsion about the C-C bond between atoms 2 and 3 will not be rotated when building the system. You might want to try OpenBabel, a toolkit that allows conversion between different molecular file formats. I have an experimental module that converts PDB to the required z-matrix format, but it needs more testing before I can deploy it in the tool.

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      Alexander Pushkarchuk

      Hi Benjamin! Thank you. I have used OpenBabel for build the z-matrix of Polyacrylamide monomer. My question is: what is the output format of OpenBabel should I use to build the z-matrix of Polymer Modeler (I used the BGF format)? Best regards Alexander

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