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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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      Varun Gopal

      This is the z-matrix for amylose. C_3 C_3 1 1.51 C_3 2 1.51 1 111 C_3 3 2.5 2 89 1 27 C_3 1 1.51 2 111 3 -55 H_ 2 1.12 1 109 5 65 H_ 1 1.12 5 109 4 -65 H_ 4 1.12 3 93 2 -109 H_ 5 1.12 1 109 2 -65 H_ 3 1.12 2 109 1 -65 O_3 5 1.42 1 109 2 176 H_ 11 .96 5 109 1 118 O_3 1 1.43 5 109 11 -62 H_ 13 .95 1 109 5 146 O_3 2 1.42 1 109 13 62 H_ 15 .95 2 109 1 -150 C_3 4 1.53 3 143 2 124 H_ 17 1.07 4 109 3 165 H_ 17 1.07 4 109 3 -74 O_3 17 1.43 4 109 3 45 H_ 20 .95 17 109 4 167 H_ 4 1.51 3 34 2 130 O_3 3 1.42 2 111 1 55 O_3 3 1.42 2 109 1 176 C_3 24 1.43 3 109 2 137 C_3 25 1.51 24 109 3 123 C_3 25 1.51 24 109 3 -114 H_ 25 1.12 24 107 3 4 H_ 26 1.12 25 109 24 55 C_3 27 1.51 25 111 24 -176 H_ 27 1.12 25 109 24 -55 C_3 30 1.51 27 111 25 55 H_ 30 1.12 27 109 25 -65 H_ 32 1.12 30 109 27 65 O_3 27 1.42 25 109 24 62 H_ 35 .96 27 109 25 174 O_3 30 1.42 27 109 25 176 H_ 37 .95 30 109 27 169 C_3 26 1.53 25 109 24 -62 H_ 39 1.07 26 109 25 -45 H_ 39 1.06 26 109 25 74 O_3 39 1.47 26 109 25 -165 H_ 42 .96 39 109 26 -146 H_ 32 1.51 30 111 27 -55 O_3 26 1.42 25 111 24 176 O_3 32 1.42 30 109 27 -176 C_3 46 1.42 32 109 30 -134 C_3 47 1.51 46 109 32 114 C_3 47 1.51 46 109 32 -123 H_ 47 1.12 46 107 32 -4 C_3 48 1.51 47 111 46 176 H_ 48 1.12 47 109 46 55 H_ 49 1.12 47 109 46 -55 C_3 51 1.51 48 111 47 -55 H_ 51 1.12 48 109 47 65 H_ 54 1.12 51 109 48 -65 C_3 49 1.54 47 109 46 62 H_ 57 1.06 49 109 47 -75 H_ 57 1.07 49 109 47 44 O_3 57 1.42 49 109 47 164 H_ 60 .96 57 109 49 119 O_3 48 1.43 47 109 46 -62 H_ 62 .96 48 109 47 -172 O_3 51 1.42 48 109 47 -176 H_ 64 .96 51 109 48 -172 O_3 54 1.43 51 109 48 176 H_ 66 .95 54 109 51 130 H_ 54 1.51 51 111 48 55 O_3 49 1.43 47 111 46 -176 Thank You

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        Varun Gopal

        The above matrix is actually of the form C_3 c_3 1 1.51 C_3 2 1.51 1 111 C_3 3 2.50 2 89 1 27………etc..

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