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
used).
Thanks!
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
