Re: [AMBER] question about bond command

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 24 Jul 2010 17:22:44 -0700

My apologies, I was thinking of ionic concentrations (which I
know something about) rather than pH (which I don't).

Hopefully someone who does know can answer your original


> Thanks. for this my whole macromolecule is neutral now if i add ions it is going
> to be charged!! will amber accept calculations with a total charge different
> from zero? I used addions before in another work when my protein charge was
> different from zero example addions 8 Na+.

> In this specific case, there seems to be a need to protonate or something like
> this for say pH=5. How can I do this since my molecule is already built. And how
> to know if I am at low pH, or high pH?

> ________________________________
> From: Bill Ross <ross.cgl.ucsf.EDU>
> To:
> Sent: Sat, July 24, 2010 9:57:32 PM
> Subject: Re: [AMBER] question about bond command

> > I want to perform calculations at specific pH. How do I do this in Amber?

> You must calculate the number of ions to use for the box of water
> you will create, and add them with leap's addions command after
> solvation. There is no way to simply request a pH.

> Bill

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Received on Sat Jul 24 2010 - 17:30:04 PDT
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