[gmx-users] question about g_sas

[Christopher Neale]

This is actually kind of unfortunate. I'm not sure where these gromacs VDW radii come from, but they're nowhere near what I presume to be the standards (either Bondi et al. or something similar). Note that even the recent updates to the Bondi values are very minor in comparison to the differences to the gromacs vdwradii.dat values.

I don't know if vdwradii.dat has been updated recently, but my version of vdwradii.dat contains the text:

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.

which is quite wrong if they are also used for computing SASA. Looks to me like something that was originally devised as a quick hack for genbox (where precise radii don't matter as much) is being used in code where radii actually matter quite a bit.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 05 May 2015 19:33
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] question about g_sas

On 5/5/15 7:23 PM, Tom wrote:
> Dear GMX developers or users:
>
> What is vdw radius that g_sas uses to calculate the SASA?
>

vdwradii.dat, in $GMXLIB.

<snip>

If you trace the code here:

>          if (!gmx_atomprop_query(aps, epropVDW,
>
> *(atoms->resinfo[atoms->atom[i].resind].name),
>                                  *(atoms->atomname[i]), &radius[i]))

epropVDW will assign properties from vdwradii.dat.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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