Re: [AMBER] constant pH simulation (protonation state specification)

From: Jason Swails <>
Date: Sun, 13 Jun 2010 12:40:57 -0400


In my opinion, you typically don't need to specify the -states flag, as you
can let the states kind of "choose themselves" during your restrained
heating (just make sure that you use the cprestart as the cpin for the
following simulation. The only time you may have to is if, for instance, 2
carboxylates are forming a very tight salt bridge, in which case you may
have to protonate one of them. However, you can just modify the RESSTATE
list in the CPIN file after it's created (you don't have to specify

Also, unless you modify, -system does nothing really unless you
specify HEWL (as that is the only system for which experimental pKa data was
put into However, you can use virtually all flags together (unless
they are mutually exclusive) to create a CPIN file.

As for the states, different residues have different default states.
Carboxylates have 5 states: deprotonated, and syn or anti on each Oxygen.
It just so happens that state 0 is deprotonated, 1 is syn on O2, 2 is anti
on O2, 3 is syn on O1, and 4 is anti on O1. Histidine, state 0 is HIP, 1 is
HID, and 2 is HIE (3 states total). All of these are commented at the
bottom of the file, I can't remember if they're explicitly stated in
the manual.

Hope this helps,

On Sun, Jun 13, 2010 at 12:16 PM, Sangita Kachhap <>wrote:

> Hello all
> I am doing constant pH simulation at pH 4 .Should I specify the -states
> flag for
> generation of cpin file?
> In manual by default protonation state is 0: which specify
> deprotonated for ASP and GLU, protonated for LYS and TYR, doubly protonated
> for
> HIS (i.e. HIP).
> In example there is other protonation state 1, 3:
> ambpdb -p prmtop < prmcrd | -states 1,3,0,0,0,1 > cpin
> So what is mean by protonation state 1, 3
> Can I specify both -state & -system flag during generation of cpin file?
> Seeking for suggestion.
> With regard
> Sangita Kachhap
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Jun 13 2010 - 10:00:03 PDT
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