Changing my structure when reopened

In MarvinSketch, carboxylates that I designate with a negative charge have a proton
added to it when I open it in MarvinSpace or reopen it in MarvinSketch [after saving as a .pdb file]. 
Furthermore, the pyridine moiety of my ligands end up having two double
bonds on either side of the nitrogen, while the rest of the ring has
single bonds.  The program seems to change the chemical structure [where
charges are designated] if the file is saved as anything but a .mrv file.  I am trying to get a .pdb without unwanted changes.

Is there an easy fix for this?

 

 I appreciate any input as I become acquainted with marvin suite.

Dear Samson,

Unfortunately PDB format does not store bond types or charges, just atoms and coordinates. Therefore bond types are estimated from bond lengths. Consequently, if you clean your molecule in 2D, then all bondlengths will be the same, and so reopen makes all bonds single. 

MarvinSketch is compatible with most standard chemical file formats, even when charge is on. PDB is an exception without our own fault. 

Best regards,

Appreciate it