I am trying to use LigBuilder v2 (http://ligbuilder.org/) with my own fragment database created from a set obtained from Molinspiration (http://molinspiration.com/).
I ran LigBuilder but none of my 10k fragment was recognized.
Looking in the fragments files, I saw that the fragments from the LigBuilder program have a section starting with @SET that contains structure information. My MOL2 files do not have this info, so maybe this is the problem.
Any ideas about how to create a personal functional fragment database for LigBuilder?
Dear I. Camps,
regets for late reply. I have inspected manually your files and find a basic error that is the absence of a keyword ( .spc ----- makes hydrogen special ) required by ligbuilder to grow fragments. Actually ligbuilder identifies the hydrogen to replace and add best possible fragment in seed by this keyword. You can also use this keyword smartly to protect those functional groups you want to keep intact in your seed. As soon i will make a functional copy of your fragment i will fwd it to you. Till you may try out this ( Almost confident that it will work). In case of success or failure please report.
P.S. Please use .spc with hydrogen atoms only.
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