[gmx-users] ex g_sas and hydrophobicity

Jernej Zidar jernej.zidar at gmail.com
Tue Nov 25 05:32:44 CET 2014

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.

  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?

Thanks in advance,
Jernej Zidar

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