MCCE/Topology

Topology files (.tpl) are used to define residues ionization states, geometry, charges, radii, etc.

Topology parameters
Topology parameters are defined in *.tpl files. The general syntax of tpl parameter is:

1234567890123456789012345 |-||- ParamNam|Res |Atom|Param

A table of topology paramters with short description
Also see Category:Topology parameter for a list of parameters defined in tpl files

A table of topology files with short description
Also see Category:Topology file for a list of defined tpl files

Create a new tpl file

 * 1) get basic pdb info from database (http://www.rcsb.org/pdb/Welcome.do)
 * 2) grep only the required chain/residue
 * 3) make new pdb file with this info
 * 4) check in pymol to make sure that the new pdb file makes sense/is what you want
 * 5) make a new directory
 * 6) * copy pdb file into it
 * 7) * copy run.prm into it
 * 8) * edit run.prm to input appropriate pdb
 * 9) * set step 1 to be true, steps 2-4 as false
 * 10) run MCCE (should take about 5-8 mins max)
 * 11) you should now have a bunch of new files. the important ones are called "step1_out.pdb" and "new.tpl"
 * 12) * from now on you are going to be modifying new.tpl
 * 13) * you need to assign orbital types to the atoms in the CONNECT part. the only orbital types supported are: s, sp, sp2, sp2, d2sp3
 * 14) * you need to add hydrogen atoms as appropriate
 * 15) * if you have multiple conformer types, each one needs its connectivity set up. for help with connectivity visit : http://xray.bmc.uu.se/hicup/
 * 16) after the CONNECT entries are edited, run "mk_iatom new.tpl outfile.tpl" where outfile is the desired name of the tpl file.  'mk_iatom" will update CONFLIST, NATOM, IATOM, and ATOMNAME
 * 17) move outfile to the parameter directory in your tpl directory
 * 18) delete new.tpl
 * 19) run MCCE steps 1-2 (set steps 1,2 to t in run.prm, steps 3,4 should still be f)
 * 20) * check for errors in run.log and debug.log.
 * 21) * fix errors and re-run MCCE until the errors no longer show up.

to add charges...
 * 1) *run gaussian or Jaguar on your molecule to get the charges.
 * 2) *insert these results into your tpl file, taking care to match up atom names.
 * make sure spacing is accurate!!!!*

add radii
 * 1) * outside research required!!!

List of things to check

 * 1) All the conformations are made
 * 2) Connectivity is completed and correct
 * 3) * make sure everything is connected to the appropriate bits
 * 4) Use mk_iatom program to make CONFLIST, NATOM, IATOM entries
 * 5) * type : "mk_iatom filename (input)  filename (output)"
 * 6) check if the NATOM makes sense (correct # of atoms involved per molecule) if not, go back, adjust/correct the connectivity and run mk_iatom again.
 * 7) check Proton and electron value for each conformer makes sense
 * 8) * go into the bit below the ATOMNAME and check out the proton and electron values, adjust as necessary
 * 9) Calculate the reference reaction field energy and put in as RXN entry
 * 10) * get the RXN entry from MCCE step 3