Questions and Answers

0 Like 0 Dislike

Brad Grim

Monomers with >4 backbone atoms

Hello,

I am trying to build poly(ethylene glycol). I've stated the number of backbone atoms as 5 in my z-matrix, but after running the build simulation, it shows my backbone number as 4, and all the oxygen atoms within the chain were replaced by carbons.

I have also tried uploading the monomer file as a pdb, but it did not recognize the structure properly.

Here is my z-matrix layout.

5    # Number of backbone atoms
H  
C       1        1.09503
C       2        1.51373     1      110.62525
O       3        1.41973     2      109.01246     1       59.41546
H       4        0.97242     3      107.06276     2      179.79454
H       2        1.09503     1      106.87400     3      120.51373
H       2        1.09356     1      108.82446     3      237.89766
H       3        1.09411     2      110.54754     1      299.87330
H       3        1.09410     2      110.54029     1      178.94552
 

Thanks

Report abuse

Chosen Answer

  1. 0 Like 0 Dislike

    Benjamin P Haley

    I published an update to the tool, version 3.37, which seems to handle this z-matrix correctly.  The previous version was ignoring the number of backbone atoms specified in the z-matrix and using the (deactivated) input value for the tail atom, which is 4, causing the O to be dropped from each monomer as a chain was built.  Thanks for telling me about this!

    Reply Report abuse

    Please login to answer the question.

    1. 0 Like 0 Dislike

      Brad Grim

      That worked perfectly. Thank you so much for resolving this so quickly! I hope you guys decide to open source this software one day. 

      Reply Report abuse

      Please login to answer the question.

1 Responses

  1. 0 Like 0 Dislike

    Benjamin P Haley

    Your zmatrix looks fine.  Something strange is happening with the tool.  Let me investigate.  Thanks for letting us know!

    Reply Report abuse

    Please login to answer the question.