[gmx-users] g_sas Vdwradii.dat

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 7 22:50:24 CEST 2008

Xavier Periole wrote:
> 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,
>                         *(top->atoms.resname[top->atoms.atom[i].resnr]),
>                         *(top->atoms.atomname[i]),&radius[i]))
>       ndefault++;
>     /* 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).

No, this does mean that it comes from vdwradii.dat. If there are missing 
atoms you can just add them to the file. The only issue is that there 
are different sets of radii in use. Which one to use depends on the 

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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