Hi,<div><br></div><div>When I run GB I get the following message.</div><div><br></div><div><div>Can't do GB electrostatics; the forcefield is missing values for</div><div>atomtype radii, or they might be zero</div><div>
<br></div><div><br></div><div>Where are these values supposed to be. I'm using OPLS and VERSION 4.0.99_development_20090425</div><div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><br><div class="gmail_quote">
On Sun, Apr 12, 2009 at 8:19 AM, Erik Lindahl <span dir="ltr"><<a href="mailto:lindahl@cbr.su.se">lindahl@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi David,<br>
<br>
This is still in testing for now, and the parallel code in particular is still buggy, but we'll have a finished format as well as documentation and parameters for release 4.1 later this spring.<br>
<br>
Cheers,<br>
<br>
Erik<div><div></div><div class="h5"><br>
<br>
On Apr 11, 2009, at 7:30 PM, David van der Spoel wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I'm trying to play with the development version of the GBSA code, but documentation is sparse :(. I found the following code in grompp.c<br>
<br>
have_radius=have_vol=have_surftens=have_gb_radius=have_S_hct=TRUE;<br>
for(i=0;i<get_atomtype_ntypes(atype);i++) {<br>
have_radius=have_radius && (get_atomtype_radius(i,atype) > 0);<br>
have_vol=have_vol && (get_atomtype_vol(i,atype) > 0);<br>
have_surftens=have_surftens && (get_atomtype_surftens(i,atype) > 0);<br>
have_gb_radius=have_gb_radius && (get_atomtype_gb_radius(i,atype) > 0);<br>
have_S_hct=have_S_hct && (get_atomtype_S_hct(i,atype) > 0);<br>
}<br>
<br>
this checks whether reasonable numbers have been set. But where should these be specified? In the topology? How?<br>
<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><br>
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<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>
</div>