Development is ongoing but get the latest version here or give it a spin on a small protein on our online version (we are getting a larger computer so you can fragment larger molecules online)
Hi. I always want to run some modeling with FMO. Thanks for developing a tool that could make such simulations easier for GAMESS users! I am trying the FragIt online. As as test, I used a long chain alkanes, C14H30. FragIt returns only one fragment. I am relatively new to FMO. Then my question is why not FragIt decomposing the long chain alkane into multiple fragments? Can we specify the number of fragments? Thanks,
Thanks for your interesting in Fragit. :) we are very proud of our tool but as you have discovered the online-version could use more options. Right now it only works for proteins (peptide backbones), sugars (saccharides) and DNA (nucleotides).
We are working to make it better and also to use custom options for fragmentation. Your feedback is greatly appreciated and I will see if I can add what you want soon.
Hi Casper, Thanks for your reply. I thought the alkane would be much simpler given that it only contains carbon and hydrogen atoms. It would be great if FragIt can be also applied to more general types of polymer. (Protein is a type of polymer, right?) Best,
While fragit works great for proteins it currently has more trouble with very general polymers such as a long alkane chain. The problem is that there will be multiple matches which does not make chemical sense. The patterns that we use identify unique places and use that to cut. However, an alkane chain do not have any unique parts we can fragment which gives problems. We have thought about polymers and there are ideas which are promising, but right now it will not work without greasing your hands.
4 comments:
Hi. I always want to run some modeling with FMO. Thanks for developing a tool that could make such simulations easier for GAMESS users!
I am trying the FragIt online. As as test, I used a long chain alkanes, C14H30. FragIt returns only one fragment. I am relatively new to FMO. Then my question is why not FragIt decomposing the long chain alkane into multiple fragments? Can we specify the number of fragments?
Thanks,
Hi Shialchemy,
Thanks for your interesting in Fragit. :) we are very proud of our tool but as you have discovered the online-version could use more options. Right now it only works for proteins (peptide backbones), sugars (saccharides) and DNA (nucleotides).
We are working to make it better and also to use custom options for fragmentation. Your feedback is greatly appreciated and I will see if I can add what you want soon.
cheers
Casper
Hi Casper,
Thanks for your reply.
I thought the alkane would be much simpler given that it only contains carbon and hydrogen atoms.
It would be great if FragIt can be also applied to more general types of polymer. (Protein is a type of polymer, right?)
Best,
Hi,
While fragit works great for proteins it currently has more trouble with very general polymers such as a long alkane chain. The problem is that there will be multiple matches which does not make chemical sense. The patterns that we use identify unique places and use that to cut. However, an alkane chain do not have any unique parts we can fragment which gives problems. We have thought about polymers and there are ideas which are promising, but right now it will not work without greasing your hands.
Casper
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