Re: [AMBER] T-leap "does not have a type"

From: David Case <>
Date: Sun, 11 Aug 2019 12:36:06 +0000

On Sat, Aug 10, 2019, Matias Machado wrote:
>The problem is that H++ protonates HIS residues (and maybe ASP/GLU/LYS)
>without changing their names to fit the AMBER's convention (HIE, HID,
>HIP, ASH, GLH, LYH). By default tleap interprets HIS as HIE (the most
>common protonation state, see any leaprc.protein.*), then the conflict
>arises at the level of the residue library cause there are unexpected
>atoms in those residues...

I'm cc-ing to Alexey Onufriev to see if there is a fix at the H++ side; but
this can be fixed on the Amber side by using pdb4amber on the output of H++:
this will look at what hydrogens are on the histidine, and adjust the residue
name accordingly.


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Received on Sun Aug 11 2019 - 06:00:03 PDT
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