Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Justin. I had not added van der Waals of phosphor for phosphor in vdwradii.dat, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following warning:
"WARNING: could not find a Van der Waals radius for 125 atoms" I have two questions. Q1) Do I add radius of van der Waals of phosphor in vdwradii.dat ? Or Ignore this warning in this time. I couldn't find the reference that report radius of van der Waals for elements like what is in vwdradii.dat. For example see this address http://www.webelements.com Q2) would you please get me exact reference to find radius of van der Waals of phosphor that match with other elements in vdwradii.dat? Thanks in advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
