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

Louic Vermeer louic at louic.nl
Wed Jan 30 14:01:49 CET 2008

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.


> 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 
> correctly from a previous (different) question[2], virtual interaction
> sites can be used instead of hydrogen atoms to define NOE restraints.
> Now all I need to do is calculate the positions of these sites. I
> thought it might be a good idea to use the "protonate" command on the
> input structure of my peptide (.gro) and calculate the position of a new
> virtual interaction site for the NOE constraint. This new virtual atom
> would have be positioned relative to the atoms that are available in the
> gromacs all-atom forcefield because it will be added to the
> non-protonated input file.
> I tried to use "pdb2gmx -vsite hydrogens" command, but it either:
> - does not seem to recognise the atom types of the protonated input
> structure because I select the ffG43a1 forcefield for the output file.
> - creates only virtual interaction sites on my LYSH residues in a
> non-protonated input file because they are the only ones in my peptide
> that still contain protons in ffG43a1.
> This behaviour seems normal to me, but let me know if I'm missing
> something here. Maybe I'm not using pdb2gmx the right way? (more
> information below[3] )
> My questions are:
> - Can pdb2gmx generate the virtual interaction sites for me? How? And if
> not:
>     - Is the procedure described above correct, or is there a better way?
>     - Does a script/program to calculate virtual interaction sites based
>       on amino-acid protons already exist? I'm capable of writing one
>       myself, but since it takes time I only want to do that if nothing
>       is available already.
>     - Am I correctly assuming that I would add a non-charged virtual
>       interaction site without a mass (so only a position to define the
>       restraint because the proton mass and charge are already accounted
>       for in the *united*-atom forcefield)
> Thanks beforehand, I'm looking forward to my "mdrun"...
> Louic Vermeer
> IPBS / CNRS, Toulouse
> Wageningen University, Wageningen
> -- footnotes below --
> [1] http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml
> [2] http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
> [3]
> - starting from a pdb-file containing "pseudo atoms"
>    # pdb2gmx -f input.pdb -o output.pdb -inter -ignh - vsite hydrogens
>    Fatal error:
>    Atom QB in residue LYSH 1 not found in rtp entry with 13 atoms
>       while sorting atoms
> - starting from a protonated file without the pseudo atoms:
>    # pdb2gmx -f input.pdb -o output.pdb -inter - vsite hydrogens -ignh
>    No error, but only LYSH gets virtual interaction sites. Removing the
>    "-ignh" leads to an error again: Atom "HA" not found in residue LYSH.
> -- end --
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