AMBER Archive (2009)

Subject: Re: [AMBER] implicit and explicit simulation: salt effect

From: David Watson (dewatson_at_olemiss.edu)
Date: Fri Jan 09 2009 - 21:49:48 CST

On Jan 9, 2009, at 9:03 PM, Catein Catherine wrote:

>
> Dear Sir/Madam, I would like to study the salt effect for the
> binding of a neutral drug with DNA from 0M to 0.5 M of salt in a
> QUALITATIVE manner. It seems to me that I can do the GB simulation
> with salt effect considered. According to amber website, it seems
> to me that it is not a problem at all to do the simulation up to
> 0.2M salt. What about up to 0.5 M of salt for qualitative
> analysis? If I should only do the analysis with explicit solvent,
> how can I incorporate salt effects in the simulation? what is the
> command line should I used? Best regards, Cat

As to performing GB with the modified model, I would suggest that you
read the original article [Theor Chem Acc (1999) 101:426-434] and note
that the model was developed (as far as I can tell) with the GBHCT
implementation.
Several other GB implementations have been developed over the years
and I would be reluctant to use the AMBER saltcon parameter with the
GBn model, based on personal experience.
Your mileage may vary.

As to incorporation of higher concentrations, the original article
mentions that the mathematical model comes from the Debye-Hueckel
limiting law, in which case I would also be skeptical of your
intentions with regards to salt concentration as 0.5 M should be well
above the limits where that formalism holds.

With regard to explicit solvation, you could could first neutralize
your system with monovalent counterions in tleap/xleap, in which case
I would recommend that you look at the first tutorial in the series on
the ambermd.org website, which mentions a DNA system, and discusses
the influence of the phosphate in the DNA backbone on charge
considerations. Then you would have to increase/decrease the size of
your periodic box in order to adjust the concentration of ions in your
system.

During the setup of your system, you would have to determine the mean
volume that your system will eventually occupy, which would be
difficult in a periodic boundary simulation. Then you would need to
determine what you mean by "0.5 M salt", because monovalent salts will
have different equivalency than salts such as CaCl2 or KH2PO4... the
sizes of said ions would influence your decisions as well, not to
mention trying to parameterize some of the ions in order to be
compatible with Amber force fields.

This is an interesting and enlightening question, and I can't wait to
hear from Case and Simmerling, because I could use some education on
this matter, as well.

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