[gmx-users] What algorithm does g_sas use?

[jia jia]

Thanks Matt!  I've seen some vmd tcl scripts using msms to get the
surface area. However I think as gromacs using united atom, I need too
change radii parameters or in a more simple way, add all hydrogen back
before  calculation....

Cheers
Guang


2012/11/8, Matthew Zwier <mczwier at gmail.com>:
> Hi Guang,
>
> Be careful with this tool. It's very fast and very good at what it's
> designed to do, but it does not appear to be designed to give accurate
> single-residue SASA (as you will read in the paper on the method employed).
> Definitely use g_sas for entire proteins or large cavities (it's blazing
> fast), but consider MSMS or DSSP for single-residue data.
>
> Matt Zwier
>
>
> On Wed, Nov 7, 2012 at 1:26 AM, jia jia <jzg579 at gmail.com> wrote:
>
>> Thanks!  I've checked  gromacs v 4.5.5 and got it.
>> Seems all version before 4.0.5 doen't have that information..
>>
>> Cheers
>> Guang
>>
>>
>> 2012/11/7, Justin Lemkul <jalemkul at vt.edu>:
>> >
>> >
>> > On 11/7/12 1:18 AM, jia jia wrote:
>> >> Dear gmx users:
>> >>     So sorry for bother you. Does any one know what algorithm g_sas
>> >> use? There is no information about algorithm in help file, man page,
>> >> and code. I think gromos use naccess method but not sure  gromacs  use
>> >> the same one.
>> >>
>> >
>> > References are printed in the screen output when running g_sas.
>> >
>> > -Justin
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Research Scientist
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > --
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