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 On Wed, Apr 20, 2011 at 3:34 AM, Victor Ruehle <[email protected]> wrote: > 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 <[email protected]>: > > 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 > > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
