I am generating small molecule parameters using PRODRG and ABT. Why exactly does PRODRG take less time then ABT? I want to know this because I am trying to decide if it is worth it to wait for ABT to run.
If there are existent structures on ABT that have different conformations than mine (but is the same small molecule), can I still use it?
If there are existent structures on ABT that have different conformations than mine (but is the same small molecule), can I still use it?
if your molecule is the same but have a different conformation, there is no problem in to use the ATB files. but for conformation what you mean? 3-D position in the space of the small molecule? in any case if the atoms componing your and ATB molecule are the same , than you can use the molecule in ATB. don't forget to add information in files of gromacs. the necessity to generate a topology files for gromacs are required for molecules with special AA. not contained in gromacs. if your small molecule si formed by canonical 20 amino acids is not necessary generate topology files Gromacs is capable to work.
best
andrea
If can also try Acpype topology generator, which is very fast if you have partial charges already.
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