[gmx-users] g_sas Vdwradii.dat

Xavier Periole X.Periole at rug.nl
Sat Jun 7 22:32:29 CEST 2008

On Sat, 7 Jun 2008 15:04:34 -0400
  "maite lopez cabezas" <lopezmai at gmail.com> wrote:
> Hi:
> I'm using g_sas *to analyse a DPPC simulation but it gave the next warning:
> WARNING: could not find a Van der Waals radius for 128 atoms
> 3840 out of 6400 atoms were classified as hydrophobic
> I saw that the **Van der Waals radius for phophorous atoms doesn't
> appear in vdwraddi.dat. When I modified it and add the **Van der Waals
> radius* for this atom and then it works well. But, where were taken
> the *Van der Waals radius* for Gromacs? Somebody knows the phophorous
> radius for gromacs?
If I am not mistaken the radius used by g_sas are actually defined within
the code and it does not use the ones given in cdwradii.dat.

have a look a the code you'll find them easily.
> In the literature appears some valors and there aren't the same for
> this programs, such as:
> Gromacs         Other
> N     0.110    0.155
> O     0.105    0.152
> Thank you in advance,
> Maité

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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