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Varun Gopal

Proper z-matrix format

Dear Sir

I am finding it hard to make the z-matrix. I see that the z-matrices of all polymers within the tool starts with H as the initial atom. Open babel can give me the matrix arrangement I need, but for my polymer under study (amylose) the matrix begins with a C atom (using open babel). When I upload it in PM, it says ‘Child Process exited abnormally’. Can you please tell me how to rectify this problem? I am new to this and I need help.

Thank You

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    Benjamin P Haley

    Hi, Thanks for using PolymerModeler! This is a common issue, and I’m working on a module that would let you upload, say, a PDB file or an XYZ file rather than a z-matrix. For now, can you post the z-matrix you are trying to use, or a PDB file of the monomer? I can try to generate a z-matrix for you in the expected format. Please add any posts to this question, or submit a support ticket to nanoHUB.

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