DVD's E-Z Guide to Top and Par Files for Heteros

This page was taken straight out of a response to a CCP4BB question answered by Gerard Kleywegt (aka DVD) as to how to find X-PLOR/CNS topology and parameter files for "acarbose". This approach can of course be adapted for any sort of heteroatom or modified amino-acid (e.g. hydroxy-Proline).

  1. go to HIC-Up ( http://xray.bmc.uu.se/hicup/)
  2. click on "Search HIC-Up"
  3. enter "acarbose" in the Google search box and click the search button
  4. this gives four hits (ACR, ABD, ABC, GAC); select the one that you want and click on the corresponding link
  5. this gives you the HIC-Up page for your compound with loads of information and links
  6. to run the PRODRG server on your acarbose compound, scroll down and hit "Run PRODRG"
  7. in many cases, the PDB file you get out of PRODRG will have more sensible geometry than the one found in the PDB; save it in a file
  8. select the "HIC-Up server" and upload the new coordinate file to get CNS, O, etc dictionaries calculated using the new coordinates
  9. save this e-mail so you'll be able to find it again next time you need dictionaries for a hetero compound