Dear Amber community,
I'm trying to figure out how LEaP concepts work. Please, check the script I wrote to build isolysine residue (lysine which forms amide bond with ε-N-atom), is it correct? I will really appreciate any help
source leaprc.protein.ff19SB
source leaprc.gaff
LYX = copy LYS
set LYX name "LYX"
set LYX.1 name "LYX"
# terminal nytrogen
set LYX.1.NZ type n3
set LYX head LYX.1.NZ
set LYX.1 connect0 LYX.1.NZ
# terminal hydrogens
remove LYX LYX.1.HZ3
set LYX.1.HZ1 type hn
set LYX.1.HZ2 type hn
# build peptide
p = sequence { ALA LYX ALA LYS }
Also I have a question: I've found in the documentation that water parameters must be sourced after macromolecular parameters, in which order must I source custom and GAFF parameters?
— Vsevolod
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Received on Fri Aug 18 2023 - 09:30:02 PDT
