[gmx-users] g_sas and f_index

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 31 09:25:54 CEST 2007

David van der Spoel wrote:
> 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).

Ahh, I went digging in the source code. The atom types are used for 
getting vdW radii (and estimating free energy of solvation, if that is 



More information about the gromacs.org_gmx-users mailing list