[gmx-users] g_sas Vdwradii.dat

maite lopez cabezas lopezmai at gmail.com
Mon Jun 9 18:54:36 CEST 2008

Thanks for the quickly answer. The problem is like David said. g_sas use
the Van der Waals radius of the vdwradii.dat file. I want to use the same
valors that appear in this file but i want to know where they were taken for
adding the P valor.


On Sat, Jun 7, 2008 at 4:50 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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 application.
> --
> 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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