Hi Amber community,
Just wanted to point something out, as i was running on my system, in hopes of helping the community. For this tutorial, in the step of preparing of the mainchain file
HEAD_NAME N1
TAIL_NAME C3
MAIN_CHAIN CA1
MAIN_CHAIN C1
MAIN_CHAIN N3
MAIN_CHAIN CA3
OMIT_NAME H2
OMIT_NAME HN11 (Should only choose 1?)
OMIT_NAME OXT
OMIT_NAME HXT
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0
Why would we want to omit both Nitrogens hydrogen when we should only remove 1 H to mimic a peptide bond (unless i lack some knowledge on modified amino acids).
Also while im asking questions on this email, i was curious on how exactly MCPB handles 2 metal centers? I havent tested it yet but was hoping to gain insight before i run it myself
Thanks in advance 🙂
Kind regards,
Ingso
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Received on Wed Jul 03 2024 - 10:00:02 PDT
