I have successfully installed AmberTools19 on my Macbook and all tests passed. I can cue Antechamber and the command:
antechamber -fi pdb -i testpdb2.pdb -o mol2 -fo mol2 -c bcc
...runs just fine.
But when I try to run:
antechamber -fi pdb -i testpdb2.pdb -o mol -fo charmm -c bcc
I get the following error:
sh: /Users/madmarchhare/amber18/bin/charmmgen: No such file or directory
/Users/madmarchhare/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/Users/madmarchhare/amber18/bin/charmmgen -i ANTECHAMBER_PREP.AC -f ac -o mol -r MOL".
I note that there's a charmmgen.c file in the directory amber18/AmberTools/src/antechamber
... but I don't have python version :(.
im just an undergraduating student but i had a chance to take a look at the documentation of Antechamber and found this: http://ambermd.org/antechamber/ac.html . there is no supported file format for "CHARMM". i hope it gives you some idea :(
Update: I reached out to the author of the paper I'm trying to replicate and it turns out the solution is simple. Newer releases of AmberTools don't compile charmmgen automatically but if your AmberTools installation was done correctly on a MacOS, you can go to the directory amber18/AmberTools/src/Antechamber and run "make charmmgen", then copy the charmmgen file to amber18/bin.
- Badges
- Science topic
- Similar topics
- Filing