[AMBER] Fundamentals of LEaP Tutorial

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Tue, 25 Aug 2020 12:36:19 +0000

It has been a long while since I tried running through the amber tutorials. Remembering the frustration trying to do the grimaces tutorials after the major command update (gmx command) with deprecated modules and more, I though I could make this a hobby project for the fall and see if I can get through them.

Having gone through the content of the “Fundamentals of LEaP” tutorial I had some suggestions and a question:


Suggested edit to the text, not sure tough it feels like the text suggests that formod should be the “abbreviation":

    well as frcmod.ff14SB (an auxiliary parameter file which has FORce field MODifications).
    well as frcmod.ff14SB (an auxiliary parameter file which has FoRCe field MODifications).

Maybe adding the pdb4amber command recreating the files
    pdb4amber -i 1FSC.pdb -o 1fsc_amb.pdb -y

I don't know if this is an OS related issue though I have noticed that the TER flag gets appended with the first there fields of the residue information from the residue prior to the TER entry when running pdb4amber. Does not really make a difference practically tough maybe someone has some insights regarding this. Example from a diff below with my “extra info” in the output to the left:

    TER 464 TYR A 61 | TER

Best regards
// Gustaf

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Received on Tue Aug 25 2020 - 06:00:02 PDT
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