[gmx-users] Regarding difference in SASA values using GMX versions 5.X and 4.X

[bipin singh]

Thanks Mark for your comments.


------------------------------
Thanks and Regards,
Bipin Singh

On Thu, May 28, 2015 at 9:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Thu, May 28, 2015 at 5:23 PM bipin singh <bipinelmat at gmail.com> wrote:
>
> > Hi all,
> >
> > I have calculated SASA for a group amino acid residues using GMX versions
> > 5.0.1 and 4.6.3 and noted that there is significant difference in the
> > calculated values, as can be seen in figure at the link below.
> >
> >
> >
> https://drive.google.com/file/d/0ByHdYJNF-aRrTEFtNDR5dEEyZlU/view?usp=sharing
> >
> > I know that it is already mentioned that from version 5.0 GMX uses the
> Van
> > der Waals radii from paper "A. Bondi, van der Waals Volumes and Radii, J.
> > Phys. Chem. 68 (1964) pp. 441-451", and it is expected to be different
> > compared to previous GMX versions. However I wanted to know what was the
> > source of Van der Waals radii in GMX 4.X versions
>
>
> History is silent, so probably someone made stuff up in a vaguely plausible
> manner.
>
> and which one is
> > considered to be more accurate.
> >
>
> "Accurate" depends on the purpose, and requires someone to show that
> certain radii correlate best with whatever other quantities. (How big is an
> electron cloud, anyway?) For observing qualitative differences in solvent
> accessibility of two configurations, probably any guess is as good as
> another...
>
> Mark
>
>
> >
> > ------------------------------
> > Thanks and Regards,
> > Bipin Singh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>