AMBER Archive (2004)

Subject: AMBER: general questions

From: Marsita M (
Date: Mon Sep 06 2004 - 10:58:34 CDT

dear list,

i have a few general questions about amber, and i hope someone can help me
answering this question

1) How to know the correct protonation state for histidines before we create
the prmtop file? does it require knowledge in chemistry? (which i'm
absolutely lacking since my background is not chemistry) .. what would
happen, if we misinterpret the correct histidine protonation site? such as
HIE instead of HID etc.

2) since i'm new to amber and my chemistry is very bad, i have one silly
question to ask, is it appropriate to neutralize the system if the
simulation is to be run in vacuo? or it wouldnt make any difference at all
since it's in vacuo where it would have been if it were to run in water?

thank you in advance

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