Hello Maria-- > > as you hinted at in your reply, I am trying to obtain per-residue > EEFx energies by using eefxpot's selection facility to select the > atoms of one residue at a time, in the manner illustrated by the > Python script below: > > # calculate subset EEFx energies (using atom selection) > for k in xrange(residCount): > rn = residList[k] > selstr = "resid %d and not name H*" % rn > eefxpot = create_EEFxPot( "eefxpot", selstr, paramSet=param_LK ) > energy = eefxpot.calcEnergy() > energySum = energySum + energy > subsetEEFx[rn] = energy > # calculate total EEFx energy > eefxpot = create_EEFxPot( "eefxpot", "not name H*", paramSet=param_LK ) > totalEEFx = eefxpot.calcEnergy() > > However, the sum of per-residue EEFx energy terms (in 'energySum') > always deviates substantially from the value obtained by evaluating > the EEFx potential over all residues at once (in 'totalEEFx'). In > the case of the gb3_refined_IV.pdb structure included in the > xplor-nih distribution the overall EEFx energy evaluates to > -955.9676, whereas the sum of per-residue EEFx terms evaluates to > -21310.651. >
Unfortunately, this sort of scripting approach does not work, due to the effects of neighbors which are not in the specified residue. One way of thinking about this is that the presence of neighbors changes the effective solvation, hence the energy. To achieve your goal, the contribution to each residue should be accumulated as the energy is calculated with all atoms, and this is something which could be easily done at the C++ level. > Since, as I understand the description of the EEFx potential in the > paper presenting it (Tian, Schwieters, Opella and Marassi , 2014), > the EEFx potential includes the classical Xplor potentals BOND, > ANGL, DIHE, IMPR, ELEC, VDW in addition to SLV (Eq 2, > pp. 55). Therefore, I have also obtained per-residue values for > BOND, ANGL, DIHE, IMPR, ELEC, VDW by using 'constraints interaction’ > statements to evaluate these potentials for suitable subsets of > atoms. Unfortunately this did not give me any hint towards > understanding the differences in EEFx values mentioned above. > The version of EEFx in Xplor-NIH 2.38 now includes the ELEC and VDW portions of the energy- there are slight inaccuracies and definite inefficiencies with the previous method we used. This does not change the fact that per-residue energies for each of these term can be accumulated by slightly modifying the C++ code. Please contact me if you are interested in having this change made. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
