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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
