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

[xin liu]

Thanks Mark, I will try that out :)

On Mon, May 5, 2008 at 12:01 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
wrote:

>  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
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