[gmx-users] g_sas Vdwradii.dat

Xavier Periole X.Periole at rug.nl
Sat Jun 7 22:43:33 CEST 2008

On Sat, 07 Jun 2008 22:32:29 +0200
  "Xavier Periole" <X.Periole at rug.nl> wrote:
> 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.
I just had a look at the code. What I said is valid for the gmx-3.1.4.
In gmx-3.3.3 you have:
   /* Get a Van der Waals radius for each atom */
   ndefault = 0;
   for(i=0; (i<natoms); i++) {
     if (!query_atomprop(atomprop,epropVDW,
     /* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
     radius[i] += solsize;

where you can see that the line I was referring to is commented and the
lines above it have been introduced to get the radius from the topology
(I think).
Check the version you use ...
>> 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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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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