Treating Multi Chain Proteins

From: Roy Fernando (
Date: Tue Sep 11 2012 - 14:58:14 CDT

Hi All,

 "I read in the NAMD documentation that it is required to separate protein
chains if your system is a multi unit system."

Can somebody shed some light in this direction.

I have a protein dimer. I am going to squeeze the two units together and
see the result. I can separate the two chains and prepare a two pbd files.
But should I prepare two psf files as well? Or am I preparing a single psf
file with two separate protein chain inputs. If that is the case, I wonder
what is the difference I can make by keeping the original pdb file with two
chains and making a single psf file.

I greatly appreciate any help.



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