AMBER Archive (2008)

Subject: AMBER: questions about run MD at different pH

From: Kailee (
Date: Mon Mar 03 2008 - 08:51:40 CST

Dear amber users,

I would like to run MD simulations of a big protein at different pH
conditions with AMBER8/9, and I have a few questions about this:

1) If I protonate my protein (which is solvated in water explicitly) with
H++ program at different pHs and then run them in AMBER as normal, at which
pH will be my protein simulating? will it be the pH value I set in H++
program OR there is a fixed pH for all simulations in AMBER?

2) I have read the manual about constant pH calculations, which can be used
for simulations at different pH, right? however, it's only for implicit
solvent simulations, and I would like to ask, is there any other differences
with this method except it can't be used for explicit solvent, for example,
I have some non-standard residues ( which I have created frcmod file for
them), will these be OK with the method? and are there any differences in
analysis methods?

3) Will it be possible that I manually add some H+ or OH- ions to change the
pH conditions? and if yes, how should I do it? should I add them in leap or
include them in the pdb file? and after the addition of those (H+/OH-),
should I still neutralise the system (using PBC)?

Thank you very much in advance!

With my best regards,

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