Hello, Everyone
It's me again! So, this email is more of a conceptual issue I'm having with both dealing with a forcefield (in this instance the GAFF) and trying to get X-Leap to recognize the individual units I'm trying to stitch together with T-Leap.
These issues I think are tied together. I found a tutorial that I thought was getting me to my goal where I was inputting atom types with the gaff atom type style into the molecule table in X-Leap and it would develop a library file that was supposedly supposed to then reference the compilation of atoms into a specific unit to be stitched together. However, I discovered that the library file has a coordinate section dedicated to the positioning of that unit and when I stitch multiple together it doesn't translate them (connect them head to tail) but rather overlaps them because of the coordinates. My issue is specifically that without the library file X-Leap doesn't recognize my structure as a unique unit like an amino acid, but with it, it doesn't actually create the polymer I'm needing.
This leads me to the idea that perhaps I need to develop a new forcefield file, but what I'm not understanding is why I would need to create a new forcefield file that is just a subset of the bond types and angles from the overall gaff force field. This has me believing that there is a third hidden option that I don't know to consider.
Hopefully this is all clear and again I appreciate any and all insight into the issue!
Thank you.
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Received on Fri Apr 23 2021 - 12:30:02 PDT
