These are not easy questions to answer. Certainly atoms, particularly ones that are charged, even with fractional charges, have a strong effect on the ESP. If you delete them because you don't know exactly where they are you will get a different answer than if you put them in in some reasonable but unsupported location (as you have found). This result indicates that the peptide does affect the ESP significantly and you have to consider it.
You could build lots of models with the peptide in different conformations and average all the maps. This misses the point. You have uncertainty in your model which means that you have uncertainty in your electrostatic potential. Any particular ESP that you calculate and draw conclusions from will have a large uncertainty and you must consider that uncertainty when deciding between your potential conclusions. (I'm not sure if the pun is intended or not!) I suppose you could believe that each possible conformation exists to some extent in reality which means that all the ESP's you calculate exist in some fraction of the molecules in the cell. It is possible that only the molecules with a particular conformation of this peptide have the ESP that allows the molecule to function. Life is hard. Another issue that you must consider: If the exact conformation of this loop causes changes to the ESP that you consider significant to your understanding of the function of this protein, the presence and conformation of neighboring proteins and solvent will also cause significant changes to the ESP. The biological context of the protein becomes important. If your interpretation depends critically on the value and distribution of ESP then I'm not sure you can work this out based on calculated ESP, considering the large uncertainty. Dale Tronrud On 12/1/2017 10:02 AM, chemocev marker wrote: > Hi > > I am calculating the Electrostatic Potential of my protein. But there > were few flexible region with high B-factor and I deleted that part of > the protein and then recalculated it. But there I can see a big > change.As I have a structure in the presence and the absence of the > peptide and the these flexible regions have a better map in the > structure without peptide and with peptide I have to delete them. > I have a question, should I model these missing regions > > or > > I should ignor them > > best > > Jiri
