Elaine: Most sorry that you had to repeat. I succeeded now, with still a problem. I.e, the membrane lipid (POPC) is hydrated at the head (this is how it can be built with the plugin). Those molecules of water are still in the space cleaned from lipid molecules, i.e. they superimpose the protein. I am not sure if such water should be removed before solvating the system, adding ions and MD. If it should be removed, is is another command? Before posting, I have now checked the saved file for the membrane. Probably there is a more serious problem: all "TER" records inserted between the POPC residues and between the WAT residues have been removed on saving (using "Save relative to model"). That will create problems to Amber, unless lack of TER records is accounted for by the CONECT records added (in the membrane pdb file from the plugin I had to add all mentioned TER records to have the file accepted by Amber) Thanks francesco In contrast, the "TER" record between the protein and the single WAT molecule within the pore was not removed. --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, You can always view the chimera-users archives to see old messages, http://www.cgl.ucsf.edu/pipermail/chimera-users/index.html
Here is the message describing how you can remove the overlapping molecules BEFORE you write the PDB file from Chimera http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 002010.html
and the one that mentioned writing PDB http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ 002008.html
I didn't say much about writing PDB, but to retain the spatial relationship you have generated in Chimera, you must choose the option to "Save relative to model" and save both models relative to the same number (if they are in 0 and 1, either save both relative to 0 or save both relative to 1, it doesn't matter which). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb
Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Nov 21, 2007, at 9:24 AM, Francesco Pietra wrote:
Elaine: Relating to your instructions of last 19 Nov (I printed your mail, then unfortunately I deleted it) how to align a protein into a membrane (for both I have valid pdb and valid Amber parameters) I am probably made elusive mistakes at the stage of saving new pdbs.
I aligned the protein into the membrane, then (with protein selected and membrane not active) I saved the new pdb, getting two files, "0" for the membrane and "1" for the protein.
In Amber LEaP both these pdb file could be loaded and combined, however save top/crd failed because something was wrong with the membrane file. In fact, if the original pdb for the membrane is used, top/crd can be saved, though the protein is not accurately aligned.
Clearly, my plan is to remove superimpositions among molecules for the "whole" obtained from Amber. Thanks francesco pietra
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