[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:
> 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
> 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).
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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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