Hi: <br>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.<br>
Thanks,<br><br>Maité<br><br><div class="gmail_quote">On Sat, Jun 7, 2008 at 4:50 PM, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c">Xavier Periole wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Sat, 07 Jun 2008 22:32:29 +0200<br>
"Xavier Periole" <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Sat, 7 Jun 2008 15:04:34 -0400<br>
"maite lopez cabezas" <<a href="mailto:lopezmai@gmail.com" target="_blank">lopezmai@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi:<br>
I'm using g_sas *to analyse a DPPC simulation but it gave the next warning:<br>
WARNING: could not find a Van der Waals radius for 128 atoms<br>
3840 out of 6400 atoms were classified as hydrophobic<br>
<br>
I saw that the **Van der Waals radius for phophorous atoms doesn't<br>
appear in vdwraddi.dat. When I modified it and add the **Van der Waals<br>
radius* for this atom and then it works well. But, where were taken<br>
the *Van der Waals radius* for Gromacs? Somebody knows the phophorous<br>
radius for gromacs?<br>
</blockquote>
If I am not mistaken the radius used by g_sas are actually defined within<br>
the code and it does not use the ones given in cdwradii.dat.<br>
<br>
have a look a the code you'll find them easily.<br>
</blockquote>
I just had a look at the code. What I said is valid for the gmx-3.1.4.<br>
In gmx-3.3.3 you have:<br>
/* Get a Van der Waals radius for each atom */<br>
ndefault = 0;<br>
for(i=0; (i<natoms); i++) {<br>
if (!query_atomprop(atomprop,epropVDW,<br>
*(top->atoms.resname[top->atoms.atom[i].resnr]),<br>
*(top->atoms.atomname[i]),&radius[i]))<br>
ndefault++;<br>
/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */<br>
radius[i] += solsize;<br>
}<br>
<br>
where you can see that the line I was referring to is commented and the<br>
lines above it have been introduced to get the radius from the topology<br>
(I think).<br>
</blockquote>
<br></div></div>
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.<br>
<font color="#888888">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div>
<div></div><div class="Wj3C7c"><br>
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