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Kortemme-Lab / flex_ddG_tutorial

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Flex ddg crashes when two chains are specified to move. #13

Closed daipayans closed 3 years ago

daipayans commented 3 years ago

Hi, I get the following message in ROSETTA_CRASH.log :

InterfaceDdGMover needs to have chains (numbers or names) or jumps defined to move

Please advise on how to proceed. Many thanks in advance!

kylebarlow commented 3 years ago

One easy thing to try would be to invert the invert the chain selection - for example, if your input PDB has chains A, B & C, try specifying "C" instead of "A,B". Does that help? If not, seeing the Rosetta script and command line call you are attempting would be helpful.

daipayans commented 3 years ago

Hi @kylebarlow, Many thanks for the quick response. Moving single chain (for eg. "A" in my case for complex AB) seems to work ok so far (running for 3 hours without crash log).

However, based on your response, I have a follow-up question, specifically related to the tutorial example on site mutagenesis. My question is that should we move a single chain or both chains? If both chains cannot be moved during a single flex-ddG simulation, which of the two chains should we select? Thanks again for your help.

kylebarlow commented 3 years ago

You only want to pick a single chain to move, as this chain will be translated far away in the simulation in order to simulate the unbound state. Picking either chain works!

daipayans commented 3 years ago

Thanks for the explanation! I was confused based on the description in the readme for "chainstomov" wihch says "Can be a single chain as in "B" or multiple chains, as in "L,H"."