Strip water molecules from all topology/coordinate files in current database about freesolv

[jchodera]

Which topology/coordinate files in particular are of interest? The Amber ones?

I might have some time to make progress on this today.

[davidlmobley]

This should be the GROMACS ones, as I always solvated things after
converting to GROMACS.

On Fri, Apr 17, 2015 at 10:25 AM, John Chodera [email protected]
wrote:

Which topology/coordinate files in particular are of interest? The Amber
ones?

I might have some time to make progress on this today.

—
Reply to this email directly or view it on GitHub
#21 (comment).

David Mobley
[email protected]
949-385-2436

[jchodera]

Is a workflow in which we first solvate in AMBER tleap and then use acpype to convert to gromacs acceptable, or would that generate undesirable topology files?

Also, if there's already an issue on the preferred way to generate these files, my apologies---feel free to just post a pointer.

[davidlmobley]

I have not validated whether acpype handles box conversions properly. (At one point in the past, it did not). So normally I just prep the molecule itself in AMBER and then solvate in GROMACS. Do you know? (We should create an issue on GitHub to lay out the protocol for re-generating everything from the source data. I'm working on figuring out who in my lab can go ahead and do this, but as noted that's a separate issue - the most immediate solution is just to strip the waters.)

[jchodera]

I don't think we can invest any time in trying to fix up manually curated files with throwaway scripts. If we do put time into this, it has to be to establish automated pipelines that build this from the ground up.

Creating a workflow to create unsolvated and solvated AMBER prmtop/inpcrd files and convert to gromacs via acpype would be pretty easy if we find this acceptable for now. There are other options too, such as using OpenMM to solvate and write a PDB file and then converting directly to AMBER and gromacs, but that might be a bit trickier right now. Eventually, these protocols can be reworked to use tools like gaff2xml once the public API is stable.

Info on acpype testing is here:
https://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx

[jchodera]

See #22

[davidlmobley]

For now, we absolutely ought to be doing the same thing we (in my group)
have always done for these which is to create AMBER files exactly as you
describe and convert to GROMACS. If you think you have time to do so today,
that's awesome. Otherwise I can put a student on it shortly.

(And, if my student for some reason takes a while to get this done, I'm not
ruling out that I will whip out a one-off script to just quickly strip the
waters so at least everything is consistent - since effectively that's what
Sereina is having to do right now anyway.)

[davidlmobley]

This was resolved by the full rebuild of the database for version 0.5, in #28 .