CHARMM Development Project Forums Active Threads This Week

Hi Rick,
Thank you for the quick response! I must admit I did read it but clearly not carefully enough! My apologies.

My plan is to use whichever lipid length covers the TM helices most completely; other than that I didn't have a strong preference other than it being something typically in a eukaryotic membrane.

The plane that is built in Step 1 already does not cover the the TM helices; when the program builds in the membrane in later steps, is it not constrained to the plane that is drawn in step 1? So, it could build the bilayer past the initial plane that is drawn, or will it attempt to pack it all in there?

Should be fixed now.

I see nothing obvious in the input; perhaps you've missed something in your careful reading of the output log file.

I generally start a new simulation when I switch ensembles.

Hi everyone,

I would like to prepare a few proteins for MD and I would like to do it on my machine. I prepare one system and I want to prepare the others applying the same protocol as charmm-gui. My problem is that charmm-gui tar.gz file has all steps needed but I do not understand how charmm-gui converts the pdb.cif to the first crd and pdb (pdb_proa.crd and pdb_proa.pdb).

Does anyone knows how charmm-gui do these conversion?

Best.