On 31/12/2011 5:04 PM, afsaneh maleki wrote:
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?
The simulation does not care about that file. Only the analysis routine
cares.
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?
Don't know.
Mark
Thanks in advance
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