Questions and Answers

0 Like 0 Dislike

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

Report abuse

3 Responses

  1. 0 Like 0 Dislike

    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.

    Reply Report abuse

    Please login to answer the question.

    1. 0 Like 0 Dislike

      Prem Shankar Gupta

      Dear Sir

      Please help me by suggesting how to construct the z-matric of monomer, as I did not find any software for constructing the same.

       

      Thanking You in advance

      Prem Gupta, India

      premsgupta.rs.bme17@itbhu.ac.in

      Reply Report abuse

      Please login to answer the question.

  2. 0 Like 0 Dislike

    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

    Reply Report abuse

    Please login to answer the question.

    1. 0 Like 1 Dislike

      Prem Shankar Gupta

      Dear Sir

      Please help me by suggesting how to construct the z-matric of monomer, as I did not find any software for constructing the same.

       

      Thanking You in advance

      Prem Gupta, India

      premsgupta.rs.bme17@itbhu.ac.in

      Reply Report abuse

      Please login to answer the question.

      1. 0 Like 0 Dislike

        Kayla f Neild

        This comment was found to contain objectionable material and was removed by the administrator.

        Report abuse

  3. 0 Like 0 Dislike

    Andrew White

    Betnacional is a leading online betting platform https://btncnl.com/app/ that has quickly gained popularity among avid sports bettors around the world. With a comprehensive range of betting options and a user-friendly interface, Betnacional provides an unparalleled gambling experience for both novice and experienced bettors alike.

    Reply Report abuse

    Please login to answer the question.