[gmx-users] Fitting when structure and reference are slightly different

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jul 9 09:13:32 CEST 2008

Hi Jochen,

If you're dealing with protein structures you can use multiprot:

I put a runner for gromacs (do_multiprot) on the user contribution page
some time ago, and can put up a more recent version if it doesn't work
with GMX 3.3.3.


Jochen Hub wrote:
> Hi,
> I run frequently into the problem that I want to fit a structure on a
> reference which is, however, not completely identical to the
> structure. The reference could, e.g., have a different protonation
> state or have an additional residue at a terminal. Is such a case a
> backbone-fit using trjconv gets erroneous since the atomic numbers of
> the backbone atoms in the two structures are not the same.
> The best solution would be the possiblity to give trjconv 2 index
> files, one giving the N fit atoms of the reference and the other the N
> related atoms (but with different atom numbers) of the fitted
> structure. As far as I know, something like that is not supported by
> gromacs so far, right?
> How do you usually deal with such a problem? Is there some more or
> less easy workaround?
> By the way, removing the atoms that do not agree in the two structures
> is not an option since I want to start a simulation from the fitted
> structure.
> Thanks a lot,
> Jochen

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