[gmx-users] NOE restraints and undefined hydrogen atoms, virtual interaction sites

[Mark Abraham]

Louic Vermeer wrote:
> In my previous message I used "all-atom" in stead of "united-atom" twice: in 
> the part about the SDS topology and again between the parentheses in my third 
> question. That's probably very confusing, so I made the corrections in my 
> quoted message below.
> Sorry for the inconvenience.
> 
> Louic
> 
>> Hi everybody,
>>
>> I want to do a refinement of an NMR structure, using NOE restraints. I
>> want to do this in SDS, using an SDS topology file[1] that was designed
>> for gromacs, but there are no explicit hydrogen atoms. I think it's not
>> a good idea to simulate a peptide with explicit hydrogens in combination
>> with an *united*-atom SDS topology (correct me if I'm wrong). If I 
> understood
>> correctly from a previous (different) question[2], virtual interaction
>> sites can be used instead of hydrogen atoms to define NOE restraints.

There's no a priori reason why a mixture of a united-atom detergent 
sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither 
is there any reason to suppose they *would* work without evidence that 
the SDS parameters were developed with this purpose in mind and suitably 
validated. For that, you'll have to read the paper referred to on the 
page you footnoted [1], I guess. Your other alternative is looking for 
an all-atom SDS topology that has been validated, but I've no idea 
whether one exists.

Regarding your footnote [2], you've provided a link to the mailing list 
search page on the GROMACS webpage, which contains multiple frames. The 
link you actually need to provide is the one to the frame that had the 
email to which you wish to refer. You can get that by right-clicking on 
that frame when it contains the content you wish.

Unfortunately I don't have the experience to comment on the rest of your 
issues.

Mark