[Chimera-users] Aligning a protein into a membrane

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 21 14:00:09 PST 2007

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.

> 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.   
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.

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