[gmx-users] Re: gmx-users Digest, Vol 114, Issue 91

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Thu Oct 31 13:45:46 CET 2013

I think ProDy can do this. It is a python module for analysis of
structures that can be downloaded from http://www.csb.pitt.edu/ProDy/
I'm not sure it can read xtc but you can probably use it after converting
trajectories to pdb.

>> On 10/30/13 11:26 AM, Knapp Bernhard wrote:
>>> Hi users,
>>> I was wondering if there is an easy and quick way to get a frame-wise
>>> binding
>>> energy between 2 groups of chains (chain ABC vs DE) in an existing
>>> trajectory.
>>> This is not indented to be an actual binding free energy approach but
>>> rather a
>>> rough indicator if the binding between two chains increases or
>>> decreases during
>>> simulation time. This should work like a protein/protein docking
>>> scoring
>>> function which assigns binding scores to single conformations. Is
>>> there a direct
>>> approach on an existing xtc (even if water was removed and not all
>>> steps were
>>> written)? Maybe like g_hbond but in addition with terms like Gvdw,
>>> Gdeformation,
>>> Ghydrophobic etc. Alternatively (and probably much more time and
>>> resource
>>> consuming), would it be possible to obtain this by the rerun option of
>>> mdrun
>>> (adjusted energy monitoring groups (the original setup was "energygrps
>>> =
>>> protein    SOL"))?
>> Using energygrps is the closest you'll get without modifying the code.
>> You'll
>> get decomposed short-range nonbonded terms, which can perhaps provide
>> some
>> indicator of the strength of the interaction between the two entities.
>> -Justin
> Hmm ok if Gromacs does not provide something like this then I ask the
> question a little bit different: Does someone know a pure scoring
> function for protein/protein interaction? It should not be a complete
> docking program but rather something which can simply evaluate given
> conformations (coming from an MD trajectory) ... and it should also not
> be a webserver (like ClusPro) but a downloadable binary because I want
> to test a quite high amount of conformations. Something like XSCORE [J
> Comp Aid Des, 16: 11-26. 2002] but instead of ligand/protein for
> protein/protein interactions.
> Cheers,
> Bernhard
> --
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