[gmx-users] g_sas vdwradii.dat

[afsaneh maleki]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111231/285019b3/attachment.html>