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On 31/12/2011 5:04 PM, afsaneh maleki wrote:
<blockquote
cite="mid:CAOXtCitDmOWewBSEStbsFKT5ssNrodL+z5FLJ91o4j0-ufuz+Q@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
The simulation does not care about that file. Only the analysis
routine cares.<br>
<br>
<blockquote
cite="mid:CAOXtCitDmOWewBSEStbsFKT5ssNrodL+z5FLJ91o4j0-ufuz+Q@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true" 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>
</blockquote>
<br>
Don't know.<br>
<br>
Mark<br>
<blockquote
cite="mid:CAOXtCitDmOWewBSEStbsFKT5ssNrodL+z5FLJ91o4j0-ufuz+Q@mail.gmail.com"
type="cite"><br>
Thanks in advance<br>
<br>
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<br>
</blockquote>
<br>
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