Comments (3)
I think we should break this a few three separate issues to make it easy to tackle these one at a time:
Trajectories
- Generate explicit solvent trajectories for all compounds
- Generate implicit solvent trajectories for all compounds
- Generate vacuum trajectories for all compounds
Hydration free energies
- Compute explicit solvent hydration free energies for all compounds
- Compute implicit solvent hydration free energies for all compounds
Related questions:
- What format should the trajectories be made available in?
- Is it OK if all of these are generated via OpenMM?
- I presume we should use the same GAFF/AM1-BCC files, including the same exact charges; we presumably want to use the new consistent mol2 files I generate with a single script from PR #11, right?
from freesolv.
Agreed, I'll do that. Though, there is some coupling - i.e. if we were
doing all of the hydration free energies, it would be trivial to generate
the trajectories. If we are doing the trajectories it is not necessarily
trivial to do the hydration free energies.
DM
On Tue, Feb 17, 2015 at 1:35 AM, John Chodera [email protected]
wrote:
I think we should break this a few three separate issues to make it easy
to tackle these one at a time:
Trajectories
- Generate explicit solvent trajectories for all compounds
- Generate implicit solvent trajectories for all compounds
- Generate vacuum trajectories for all compounds
Hydration free energies
- Compute explicit solvent hydration free energies for all compounds
- Compute implicit solvent hydration free energies for all compounds
Related questions:
- What format should the trajectories be made available in?
- Is it OK if all of these are generated via OpenMM?
- I presume we should use the same GAFF/AM1-BCC files, including the
same exact charges; we presumably want to use the new consistent mol2 files
I generate with a single script from PR #11
#11, right?—
Reply to this email directly or view it on GitHub
#15 (comment).
David Mobley
[email protected]
949-385-2436
from freesolv.
OK, so the current plan on this issue is:
- Generate explicit solvent trajectories for all compounds
- Generate implicit solvent trajectories for all compounds
- Generate vacuum trajectories for all compounds
from freesolv.
Related Issues (20)
- Decide any other supporting files/data which ought to be captured when database is re-constructed from primary data HOT 2
- Re-construct database files from primary data HOT 11
- Strip water molecules from all topology/coordinate files in current database HOT 8
- Protocol for generating solvated input files for various codes (AMBER, gromacs) HOT 1
- Have GBSA models been benchmarked on FreeSolv? HOT 4
- Migrate issues and close this repo? HOT 10
- In next update, include a json format version of database HOT 1
- Flag molecules with possibly problematic tautomers (and investigate tautomers for them)?
- Update column names to be more informative HOT 2
- Make CHARMM input files via ParmEd
- Potential duplicate molecules in FreeSolv Set HOT 12
- Set up Travis-CI testing
- GAFF version HOT 5
- Cannot generate GAFF mol2 from Tripos mol2 file HOT 2
- rebuild_freesolv.py script HOT 2
- Problems with processing some SMILES - omega returned error code 0
- Sanitize SDF files
- gromacs-mdp:with verlet lists rcoulomb!= rvdw is not supported HOT 3
- mobley_3323117 (sulfolane) has non-standard SMILES HOT 1
- Is gromacs_energies available to download anywhere? HOT 4
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