mapping for simple protein

[Sikandar Mashayak]

Hi

I am trying to define a mapping file for a simple protein. I got a pdb file for sample chain like NH3-CHCH3-CO--(NH-CHCH3-CO)n--NH-CHCH3-COO . I want to represent each monomer unit with one bead at its COM.

I am not sure how to write out mapping definition for csg_map. When I check csg_dump output for the atomistic tpr, it looks like as in attached file. I am guessing that I will have to write out definitions for all 65 beads although I have just 3 types of beads, also I will have to define the bonds,angles etc  explicitly in XML file. 

Is there any easier way out?

thanks

sikandar

[Victor Ruehle]

Dear sikandar,

unfortunately there is no way yet to automatically generate mappings
based on building blocks (similar to pdb2gmx). However, iut's on our
todo list. I so far used a script for that. It's not a big thing,
attached it. Change N to the number of units and adjust the bead
mappings.

Victor

2011/4/19 Sikandar Mashayak <symas...@gmail.com>:

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[Sikandar Mashayak]

exactly I got around the issue by writing small program to generate mappings definition for the building blocks but I didnt worry about specifying bonded interactions in CG topology as I was not going to CG those for my test case...

... thanks for the script anyway