Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unable to get the correct tleap comand with build_mixture_prmtop #277

Open
jy634 opened this issue Aug 24, 2018 · 0 comments
Open

Unable to get the correct tleap comand with build_mixture_prmtop #277

jy634 opened this issue Aug 24, 2018 · 0 comments

Comments

@jy634
Copy link

jy634 commented Aug 24, 2018

Dear Openmoltools team,
I've been trying to use openmoltools to simulate a neat liquid, yet I constantly get the wrong tleap commands that keeps on using tmp_filenames. Can someone help me understand why this might be happening? Thank you so much in advance for all your help.

I've just used the same line from test_amber.py, and each parameters have its absolute path to the filenames manually specified.
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, box_filename, prmtop_filename, inpcrd_filename, water_model=None)
Additional version info: I'm currently using python 3.6.5, Openeye 4.5.9, and current openmoltools.

RESULT :

source leaprc.gaff
source oldff/leaprc.ff99SB
MOL = loadmol2 in0.mol2
box = loadPdb tbox.pdb
loadamberparams in0.frcmod
setbox box centers
saveAmberParm box out.prmtop out.inpcrd
quit

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant