Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, 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) Can I add radius of van der Waals of phosphorous in vdwradii.dat after simulation? or should i repeat simulation again? 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
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