[gmx-users] g_sas vdwradii.dat

[Mark Abraham]

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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