Hi,<br><br>I finished the simulation of a peptide in DOPC bilayer in according to<br>tutorial by Dr. Justin.<br>I had not added van der Waals radius of phosphorous in the <br>vdwradii.dat file, when I did simulation. It seem that it use the default<br>
value of 0.12 nm.<br>When I use g_sas command, I get the following warning:<br><br>"WARNING: could not find a Van der Waals radius for 125 atoms"<br><br>I have two questions.<br><br>Q1) Can I add radius of van der Waals of phosphorous in vdwradii.dat after simulation? or should i repeat simulation again? <br>
<br>I couldn't find the reference that report radius of van der Waals for<br>elements like what is in vwdradii.dat. For example see this address<br><a href="http://www.webelements.com">http://www.webelements.com</a><br>
Q2) would you please get me exact reference to find radius of van der<br>Waals of phosphor that match with other elements in vdwradii.dat?<br><br>Thanks in advance<br>