[gmx-users] when I switch to ffG43a1, the problem occurs

[Mark Abraham]

xin liu wrote:
> Dear GMX-Users
> 
> I want to perform a MDS with lignd solvted in DMSO, this is how I setup 
> the top file:
> 
> #include "ffgmx.itp"
> #include "lig_ffgmx.itp"
> #include "dmso.itp"
> 
> [ molecules ]
> ; name    number
> Protein    1
> DMSO    3245
> 
> My system works fine with "ffgmx.itp". However, after I changed the 
> parameters to "ffG43a1.itp" and "lig_ff43a1.itp" accordingly, the grompp 
> command complains about "Atomtype 'SD' not found". I think this probably 
> because the program didn't recognize the DMSO atomtype, but how should I 
> setup the top file so as to include it properly and avoid the error? I 
> think I might have missed some fundamental clues when seting up the 
> FF43a1 top file.

Yep. The fundamental principle is not to mix force fields. Absent a 
cunning construction of your dmso.itp, it will be for working with one 
force field only. If you wish to change force fields (and you should, 
because use of ffgmx is deprecated) then you need to find a DMSO model 
suitable for use with that other force field. Hopefully there will 
already exist a suitable dmso.itp file, but likely you'll have to create 
such a file yourself from the parameters given. This will require a 
sound knowledge of chapter 5 of the GROMACS manual. Also check out 
http://wiki.gromacs.org/index.php/Force_Fields and 
http://wiki.gromacs.org/index.php/Parameterization

Mark