[gmx-developers] Generalized Born

[Ilya Chorny]

Hi,
When I run GB I get the following message.

Can't do GB electrostatics; the forcefield is missing values for
atomtype radii, or they might be zero


Where are these values supposed to be. I'm using OPLS and VERSION
4.0.99_development_20090425

Thanks,

Ilya

On Sun, Apr 12, 2009 at 8:19 AM, Erik Lindahl <lindahl at cbr.su.se> wrote:

> Hi David,
>
> 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.
>
> Cheers,
>
> Erik
>
>
> On Apr 11, 2009, at 7:30 PM, David van der Spoel wrote:
>
>  Hi,
>>
>> 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
>>
>>  have_radius=have_vol=have_surftens=have_gb_radius=have_S_hct=TRUE;
>>  for(i=0;i<get_atomtype_ntypes(atype);i++) {
>>   have_radius=have_radius       && (get_atomtype_radius(i,atype) > 0);
>>   have_vol=have_vol             && (get_atomtype_vol(i,atype) > 0);
>>   have_surftens=have_surftens   && (get_atomtype_surftens(i,atype) > 0);
>>   have_gb_radius=have_gb_radius && (get_atomtype_gb_radius(i,atype) > 0);
>>   have_S_hct=have_S_hct         && (get_atomtype_S_hct(i,atype) > 0);
>>  }
>>
>> this checks whether reasonable numbers have been set. But where should
>> these be specified? In the topology? How?
>>
>>
>> --
>> 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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-- 
Ilya Chorny Ph.D.
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