-
Notifications
You must be signed in to change notification settings - Fork 5
csimmerling/ff19SB_201907
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
This will explain how to install ff19SB and get it working with Amber. It will be included with the Amber release in 2020, but in the meantime this will allow you to use ff19SB with Amber18/19. Once you download the ff19SB files here, you will see these directories: amber_patch: update.201906 forcefield_files: leaprc.protein.ff19SB, parm19.dat, frcmod.ff19SB, amino19.lib, frcmod.ff19SB_XXX test: test_forcefield_parameter and test_MDengine have necessary files for implementation and energy test doc: forcefield_files How to set up ff19SB for Amber: 1. compile Amber18+AmberTools19 with all updates applied following the Amber 19 Reference Manual. You cannot use an older version of Amber. 2. go to directory ff19SB_201907 and run copy.sh, this will copy all of the ff19SB files to $AMBERHOME 3. go to $AMBERHOME and run: ./update_amber --apply-patch=update.201906 4. recompile amber following the Amber 19 Reference Manual (you must recompile or ff19SB will not give correct results!) 5. go to the test/test_forcefield_parameter, run "tleap -f tleap.input" to generate scramble.prmtop. Type "bash run.sh" and "vimdiff single_point_ene.output.ref single_point_ene.output" to check if all energy terms have identical values 6. go to $AMBERHOME/test/ff19SB, type "csh Run" to check if the CPU test passes 7. go to $AMBERHOME/test/cuda/ff19SB, make sure GPU is accessible, type "csh Run SPFP" and "csh Run DPFP" to check if the GPU test passes 8. refer to doc/forcefield_files if you want to implement a non-standard amino acid with ff19SB 9.In order to use ff19SB, source leaprc.protein.ff19SB when you run tleap or xleap. Please email us if you run into any issues: chuan.tian.1@stonybrook.edu carlos.simmerling@gmail.com
About
No description, website, or topics provided.
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published