On Sep 30, 2010, at 9:50 AM, Francesco Oteri wrote:
Dear AMBER users, I've one file with the AMBER topology of my system, but I saved some rappresentative structures as pdb. Since my system is made of a set of circular DNA, I'd manipulate pdb to obtain the correct connectivity.
There is a way to load a correct pdb ( or topology file) and exporting this connectivity on the other pdb?
For example, should be useful if I load at the beginning the correct pdb and than I'will load the remaining structure whit the same number of atoms of the first but without CONECT and/or TER tag.
There is no built-in function for this. However, I've attached a Python script that will use the lowest-numbered open model as a "prototype" and re-bond all the higher-numbered models based on the prototype (though it will skip models that don't have the same atom/ residue names as the prototype). So just open your correct PDB as model 0 and all the ones you want fixed up in other model numbers and run the script. You can run the script by opening it with File...Open or with the "open" command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu