Hi all, I recently completed several simulations of pure DPPC bilayers (128 lipids, 64 per leaflet, from Tieleman's site), and am processing the output. Of interest to me is the SASA, so I'm using g_sas. I ran the command:
g_sas -f md_0_100.xtc -s md.tpr -n sas.ndx (selecting solvent for the calculation, and a subset of my lipids for output) I get the following message: 0 out of 3200 atoms were classified as hydrophobic But yet, if I let the calculation go anyway, I get seemingly reasonable values for hydrophobic, hydrophilic, and total SASA. It is odd to me that in a membrane, none of the atoms are considered hydrophobic. Should I be concerned about my results being incorrect, or is it simply because the atom types of the acyl chains are unrecognized as standard by g_sas? I have learned not to ignore such strange messages :-) Thanks in advance. -Justin ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
