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Emanuele Silvestri

Error in generating PLA polymer structure

I'm trying to built a very simple PLA chain composed by only 3 monomers of lactic acid (LAC).
I'm new with the tool, anyway I understood after some attempts how to generate the right z-matrix for my monomer, that is

6   # number of backbone atoms
H_
O1   1 0.970
C1   2 1.436  1 109.474
C2   3 1.528  2 108.814  1  60.1
O1   4 1.359  3 111.369  2 343.9
H_   5 0.937  4 120.000  3   0.7   # added H
C3   3 1.516  2 108.735  1 300.0
H1   6 1.070  3 109.467  2  59.2
H2   6 1.070  3 109.478  2 299.2
H3   6 1.070  3 109.465  2 179.2
H4   3 1.070  2 110.650  1 180.0
O2   4 1.220  3 125.176  2 164.6


I think to have set the parameters in the right way, as well the zm file that I uploaded in PM.
Neverthless I continue to get always the same error in the Running Simulation, that is:

Expected number in line 429, but found

and nothing else.
Since there's not a debugging tool, I can't know where is my mistake.
Is anyone familiar with this kind of error?

Thanks for your support.

Regards

  1. tool:polymod

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    Benjamin P Haley

    Hi,

       The tool has an option in the Advanced tab of the structure builder to write the builder input file as an output of the run.  That will at least allow you to see what the builder is reading on line 429 of the input file.

       You may have a problem with the z-matrix.  The builder will remove the head and tail atoms, atoms 1 and N, where N is the number of backbone atoms.  It will create bonds from the tail-1 atom of the current monomer at the end of the chain to the head+1 atom in a new monomer that is added to the chain.   In your case atoms 1 and 6 will be removed, but atoms 8,9,10 are bonded to atom 6, so they will be bonded to the first atom in the next monomer, which is probably not what you want.  See the PMMA examples in the tool.  I sometimes create a single monomer chain, a single monomer molecule, to see the atom numbers of the output structure.  You can compare the structure and the z-matrix to see which atoms are removed and how the side groups are connected to the backbone atoms between the head and tail atoms.

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      Emanuele Silvestri

      Thank you, effectively I wrongly connected the atoms. Now it runs!

      I had success also with a GLA chain, but now i'm trying to built a PLGA, following the example of PMMA (atactic). This is my zm file

      5
      O   
      C   1 1.436
      C   2 1.528  1 108.814
      O   3 1.359  2 111.369  1 343.9
      H   4 0.937  3 120.000  2   0.7
      C   2 1.516  1 108.735  3 239.9
      H   6 1.070  2 109.467  1  59.2
      H   6 1.070  2 109.478  1 299.2
      H   6 1.070  2 109.465  1 179.2
      H   2 1.070  1 110.650  3 119.9
      O   3 1.220  2 125.176  1 164.6
      5
      O   
      C   1 1.432
      C   2 1.521  1 109.428
      O   3 1.358  2 111.378  1 342.2
      H   4 0.986  3 108.075  2 359.5
      H   2 1.092  1 108.475  3 241.2
      H   2 1.093  1 109.021  3 120.5
      O   3 1.220  2 125.060  1 163.1

      I have simply merged the two single zm in a unique file. Anyway the tool yields an error of "Invalid z matrix: missing information"

      Could you explain me why?

       

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        Benjamin P Haley

        Did you set the number of zmatrices to 2 in the entry above the zmatrix file box?

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        Prem Shankar Gupta

        Dear Sir

        Please tell me how you have constructed the z matric of monomer?

         

        Thanking you in advance for your valuable suggestions

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