[gmx-users] question about g_sas: dgSolv

[Justin Lemkul]

On 8/31/15 10:29 AM, ANTHONY C MANSON wrote:
> Hello:
> In the tool g_sas, what are the units of the dgSolv value that is output.  The
> plot in which they occur says that the units are nm squared (seems strange to
> me).  If this is true, how can one convert (ie. what is the conversion factor?)
> the values to KJ/mol, or is this already done implicitly in the tool?
> The code for gms_sas.c makes the query:
>        if (!gmx_atomprop_query(aps,epropDGsol,
> *(atoms->resinfo[atoms->atom[ii].resind].name),
> *(atoms->atomtype[ii]),&(dgs_factor[i])))
> and returns the factor to multiply the SASA for atom i in dgs_factor[i].  Where
> in the force-field data is this number defined and what are its units?

The data file is dgsolv.dat in $GMXLIB.  The units provided there are 
kcal/mol-A^2, thus converted easily to energy from SASA.  Not sure how much I 
trust the values, myself.  It seems the outcome can vary quite a lot depending 
on whose values you use...

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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