Re: [AMBER] radii effect on PB_cavity surften_cavity offset

From: berin karaman <berinkaraman.yahoo.com>
Date: Fri, 2 Aug 2013 00:24:37 -0700 (PDT)

Dear Ray,

Thank you very much for the comments, I really appreciate your help.

Best regards,


Berin Karaman




Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universitšt Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany



________________________________
 From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
To: berin karaman <berinkaraman.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 2 August 2013, 5:36
Subject: Re: [AMBER] radii effect on PB_cavity surften_cavity offset
 

Dear Berin,

>
> I would like to try different setups
> for PB calculations. As I will be generating my Leap files
> using different radii set (bondi, mbondi, mbondi2, mbondi3, Rmin,
> Parse) for GB calculations,

Sure you can certainly exploring different radius definitions in PB/GB
calculations, for both polar and nonpolar components.

>
> it will as I assume affect my results evetually when I use them in PB calculations with different
> INP = 1&2, RADIOPT=0&1 or I also want try hybrid models with
> IVCAP=1&5...

Yes. These will definitely change your free energies ...

>
> Is it okay
> to use default† cavity_surften, cavity_offset for PB calculations
> whenever I change the radii in xleap ?

In general, the surface tension and offset are optimized for a
specific radius set definition and vise versa. Thus you may want to
follow the original suggested combination of radius set and surface
tension/offset. Of course, the differences are often small for
nonpolar solvation energy calculations, but are large for polar
solvation energy calculations. If you want to study the effect of
different radius set or surface tension/offset, you may want to follow
the original suggestions. Nevertheless, you can certainly optimize
yourself.

There are also many efforts optimizing radii for both polarand
nonpolar PB/GB solvation energies based on different strategies. Of
course different efforts lead to different values. So it is a good
idea to see how different radius sets lead to different agreements
with experiment for your system at hand.

>
> I have prepared a small table for different setups where i change the INP, RADIOPT, IVCAP parameters by looking at the
> AMBER 12 / Examples
> /TEMPLATE_INPUT_SCRIPTS / SURFTEN_SURFOFF_Recommendations.pdf file
>
>† If anybody has experience about different radii effects on PB calculations and how we need to change the input, I will really appreciate if you can have a look at the table
> and let me know if I need to change something in the procedure.

Your table is quite extensive. If you want to look at the effect of
radii, a good starting point is the original references recommending
these values. It is simply too hard to summarize these efforts in the
manual. I think we have listed at least two references for the
PB-related radii. You can also find other references useful for your
effort in these two papers. For example, you mentioned PARSE radii in
your table, which is also cited in the following papers.

C. H. Tan, L. J. Yang and R. Luo, How Well Does Poisson-Boltzmann
Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis,
J. Phys. Chem., 110:18680-18687, 2006.
C. H. Tan, Y. H. Tan, and R. Luo, Implicit Nonpolar Solvent Models, J.
Phys. Chem., 111:12263-12274, 2007.

Basically, you are doing a research, so it is always a good idea to
start your literature study first.

All the best,
Ray

>
>
>
>
> Medicinal Chemistry
> Institute of Pharmacy
> Martin-Luther-Universitšt Halle-Wittenberg
> Wolfgang-Langenbeck-Str. 4
> 06120 Halle (Saale), Germany
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Fri Aug 02 2013 - 00:30:03 PDT
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