[gmx-users] g_sas and f_index

David van der Spoel spoel at xray.bmc.uu.se
Thu May 31 09:15:51 CEST 2007

Mark Abraham wrote:
> Hi,
> g_sas for determining solvent accessible area requires a .tpr file as 
> input, presumably to extract the charges in order to determine whether 
> atoms are hydrophobic or hydrophilic. However the -f_index option allows 
> a .ndx file to make this assignment. Thus it seems to me that these 
> options should be mutually exclusive (if there's no other function of 
> the .tpr file), or at least the .tpr should be optional if -f_index is 
> used.
> Am I missing something here?
The f_index overrides info from the tpr file but tpr is necessary for 
atom types (although that info could be taken from a pdb file as well).

> Mark
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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