--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Nov 21, 2007, at 1:14 PM, Francesco Pietra wrote:
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?
You would just use the same approach as for the lipid molecules - find some way of selecting the residues you don't want (using a distance cutoff from the protein atoms) and then delete them. Try different selecting commands similar to what I sent before and see if they select what you want. It is not possible to give the exact command without knowing all the details of your system.
I tried a lot of different combinations, without picking the right one, in order to remove water from only the zone from where POPC molecules are removed. I changed selections in Taskbar .. Select ... Zone, as if they were reflected to the command-line command or not. In all cases, it was only the command command-line command select #0 & #1 z<1.5 that worked. Of course, select solvent .. delete did not work, all WAT residues were removed. That is, I don't understand is how "select" of command "select #0 & #1 z<1.5" operates, i.e. why it only recognizes POP residues and not WAT residues in the membrane pdb. I tried to remove TER records, and even renaming WAT: in any case, only POPC were removed.
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)
It is technically correct to remove the TERs between HETATM residues, since HETATM residues in PDB format are not connected to each other unless there are CONECT records that say they are connected.
All atoms, for both POPC molecules and water molecules, are called ATOM. This was done by the plugin. (if this matters). Thanks francesco
However, AMBER may need the technically incorrect format (sounds like it does), and you may just have to put the TER lines in yourself or write a script to do that. Best Elaine
____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs