> Dear users, > > I am using g_sas to analyse simulations which contain an AMP molecule and > Mg > ion (in addition to amino acid ligands and an enzyme). When running g_sas > I > get the message: WARNING: could not find a Van der Waals radius for 2 > atoms. > I presume these two atoms are the P and Mg. Is there any way of defining > radii for these atoms?
Yes, the definitions are taken from $GMXLIB/vdwradii.dat. You could either edit that, or possibly copy it to your working directory, edit there and g_sas should pick up the local copy. This mechanism works for other such files, so I'd guess it works here too. > Also if I am comparing the SASA for the enzyme in > three different simulations were only the ligand (for which all radii are > defined) differs, would this have a huge effect on the results? Your question is not clear to me. 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
