[gmx-users] ex g_sas and hydrophobicity

Justin Lemkul jalemkul at vt.edu
Tue Nov 25 13:28:35 CET 2014

On 11/24/14 11:32 PM, Jernej Zidar wrote:
> Hello everyone,
>    I was wondering how 'gmx surface' and g_sas determine the
> hydrophobicity and hydrophilicity of a particular atom. The manual
> states it uses partial atomic charges to accomplish this, that's why a
> user must supply a TPR file. The maximum partial atomic charge of a
> hydrophobic atom in this scheme appears to be 0.2.

More specifically, 0.2 is the limit of the absolute value of the charge.

>    Does this mean that an aliphatic methyl carbon atom with a partial
> atomic charge of -0.27 (in the CHARMM forcefield) is classified as a
> hydrophilic atom?

Yes, hence why the assumption about 0.2 e is not always a good one. 
Fortunately, this is where index groups come in handy.



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


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