AMBER Archive (2009)

Subject: Re: [AMBER] Solvate in an alkaline solution

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Sep 10 2009 - 07:05:44 CDT

On Thu, Sep 10, 2009, vallespardojl_at_chem.leidenuniv.nl wrote:
>
> I want study the behavior of my molecule in environments with
> different pH values, mainly in alkaline solutions.
> Are there any option with the xleap for solvate the molecule selecting
> a concret pH?

LEaP does not do this. There are a variety of programs on the web (see, for
example the link to H++ on the Amber web site) that will estimate protonation
states of amino acids given a structure and an input pH. Once you have
those predictions, edit your pdb file to make the protonation states of the
residues match what you want; then load the modified pdb file into LEaP.

[There is also the option to set a particular pH value in "constant pH"
simulations. But that is a somewhat advanced option that should probably only
be used by those who have a fair amount of experience with more standard
simulations.]

...dac

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