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CCPBioSim / fesetup

A tool for setting up free energy simulations.
http://www.ccpbiosim.ac.uk/software
GNU General Public License v2.0
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correct_pH for complex #15

Closed velocirraptor23 closed 4 years ago

velocirraptor23 commented 4 years ago

Hi, I have noticed that when running FESetup, in the part of complexation it brings the protein.pdb to the folder instead of the protonated.pdb. If this is true then pH is not correct. What is pH by default? Is there any way to take the protonated option?

ppxasjsm commented 4 years ago

I think it should be possible to specify which pdb file to use for complexation. For example you can just run complexation on its own.

If you give details of your input config file it might be easier to track what is going on. I have no idea what exactly you are doing.

It might also be worthwhile considering to migrate to using BioSimSpace for the setup rather than FESetup.

velocirraptor23 commented 4 years ago

BioSImSpace sounds awesome, I just tried it but I'm gonna make some tests. What I'm doing is inputs preparation for SIRE. I wanted to get inputs ready at pH = 7.3 and I added propka term. I got protonated.pdb, however when the complex was made FESetup took protein.pdb again and the solvated system was made with the original pdb. Then I realized that to take correct protonation I should change name of protonated.pdb to protein.pdb before to run complexation separately.

velocirraptor23 commented 4 years ago

I think it needs to also specify pH during minimization, but before we need to change aminoacids names to specify which ones are implied on this (achieved with PROPKA). Not sure if we need to keep also pH during simulation running in SIRE.

ppxasjsm commented 4 years ago

You can use the protonated.pdb as input with BioSimSpace and then just carry on running your simulation protocol. That should work fine.

velocirraptor23 commented 4 years ago

Ok. great. Ill do that.

Bests

Cesar