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.
ppy.xml.sh
Description: Bourne shell script
