[gmx-developers] Generalized Born

[David van der Spoel]

Per Larsson wrote:
> Hi,
> 
> 11 apr 2009 kl. 19.30 skrev David van der Spoel:
> 
>> 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
> 
> Yes, sorry about that, most of this stuff is till in my head, maybe 
> something eventually needs to be on the wiki about how to run GBSA.
> 
>>
>>
>>  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?
> 
> All GB parameters are included in .itp-files that are specific to each 
> forcefield. Currently oplsaa, amber03, amber96 and charmm are 
> implemented, but I'm not sure if the actual files are commited to cvs yet.
> 

But if they are not committed, what is the syntax then? Extra parameters 
in the atomtypes section?

 From toppush.c I find:
             nread = sscanf(line,"%s%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf",
                            type,btype,&atomnr,&m,&q,ptype,&c[0],&c[1],
                            &radius,&vol,&surftens,&gb_radius);

Now the question is what do these parameters mean? Is there a paper that 
explains it?

I would just like to add an area term, no electrostatics. Any tips on 
how to accomplish that?

> Cheers
> /Per
> 
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-- 
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