Error in Fragment Generation for Polymer with Rings
- mikewelsch
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2 years 6 months ago #943
by mikewelsch
Hi there,
I am working on calculating gas solubility within different polymer materials and I'm attempting to create systems of this furan-based polymer called Poly(trimethylene 2,5-furanoate) (PTF). I'm using CASSANDRA V1.2. I did at one point run into the limitation of Cassandra that requires the starting configuration of a ring and its exo-atoms to match the MCF exactly in order for the fragment library to be generated and I did remedy that. Now I'm getting an error that I can't quite parse from the documentation or other forum posts.
When I try running the fragment library setup python script I get the result that I've copied into the attached file titled 'frag.log'. Essentially the ring fragments encounter a segmentation fault and state that some number of multiring atoms were detected and I'm not sure what that means. I can't quite seem to locate what script has info on that error. I'm attaching all relevant files needed to replicate this error.
Any help would be appreciated!
Thanks,
Micah Welsch
University of Kansas
I am working on calculating gas solubility within different polymer materials and I'm attempting to create systems of this furan-based polymer called Poly(trimethylene 2,5-furanoate) (PTF). I'm using CASSANDRA V1.2. I did at one point run into the limitation of Cassandra that requires the starting configuration of a ring and its exo-atoms to match the MCF exactly in order for the fragment library to be generated and I did remedy that. Now I'm getting an error that I can't quite parse from the documentation or other forum posts.
When I try running the fragment library setup python script I get the result that I've copied into the attached file titled 'frag.log'. Essentially the ring fragments encounter a segmentation fault and state that some number of multiring atoms were detected and I'm not sure what that means. I can't quite seem to locate what script has info on that error. I'm attaching all relevant files needed to replicate this error.
Any help would be appreciated!
Thanks,
Micah Welsch
University of Kansas
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- emarin
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2 years 6 months ago #944
by emarin
Hello Micah,
Looking at the generated MCF file, fragments 2 and 3 have 20 atoms. By looking at the molecular structure of the polymer, it seems like the fragment with the most atoms should be 9 (5 ring atoms, 2 hydrogens and 2 exoring atoms).
We have found problems with the script when identifying rings structures. This might be a case. If the script doesn't work, I'd recommend to build the fragment section manually and build the associated fragment configuration libraries without the script.
Please let us know how this goes!
Looking at the generated MCF file, fragments 2 and 3 have 20 atoms. By looking at the molecular structure of the polymer, it seems like the fragment with the most atoms should be 9 (5 ring atoms, 2 hydrogens and 2 exoring atoms).
We have found problems with the script when identifying rings structures. This might be a case. If the script doesn't work, I'd recommend to build the fragment section manually and build the associated fragment configuration libraries without the script.
Please let us know how this goes!
Please Log in to join the conversation.
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