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MCCE/Topology

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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
column 1-8 name of the parameter
column 9 left blank
column 10-14 residue or conformer name
column 15 left blank
column 16-19 atom name
column 20 left blank
column 21- formatted parameter

A table of topology paramters with short description

Also see Category:Topology parameter for a list of parameters defined in tpl files

CONFLIST
NATOM
IATOM
ATOMNAME
PROTON
PKA
ELECTRON
EM
RXN
CONNECT
RADIUS
CHARGE
ROTAMER
TORSION Torsion energies and how to build missing atoms
VDW_RAD VDW radius
VDW_EPS VDW potential

A table of topology files with short description

Also see Category:Topology file for a list of defined tpl files

Always_needed Global parameters
7MQ Menaquinone
ALA Alanine
ARG Arginine
ASN Asparagine
ASP Aspartate
BCB Bacteriochlorophyl monomer
BCL BACTERIOCHLOROPHYLL A
BCT bicarbonate
BDL
BKB Backbone
BPB.tpl
BPH.tpl BACTERIOPHEOPHYTIN A
_CA Calcium
CL1
CLD
_CL Chloride
CTR.tpl c-terminal
CUA CuA site
CUB.tpl CuB site
_CU Copper
CYD.tpl CYS making disulfide bond to another CYS
CYS.tpl Cysteine
dua.tpl di-copper site
fal.tpl
far.tpl
fe2.tpl ion
fme.tpl
fs4.tpl ion-sulfur cluster
gln.tpl Glutamine
glu.tpl Glutamate
gly.tpl Glycine
ha0.tpl heme (no ligands, old)
ha3.tpl heme a3
hea.tpl heme a
heb.tpl
hem.tpl heme (no ligands, hard charge)
hib.tpl Backbone of HIS, used when HIS side chain is a ligand
hil.tpl
his.tpl Histidine
hli.tpl
hmb.tpl heme b
hoh.tpl water
ile.tpl Isoleucine
lda.tpl LAURYL DIMETHYLAMINE-NOXIDE
leu.tpl Leucine
lhg.tpl
lys.tpl Lysine
mel.tpl
mem.tpl membrane
met.tpl Methionine
_mg.tpl Magnesium
myg.tpl
nh4.tpl ammonium ion
ns5.tpl NS5
ntg.tpl
ntr.tpl n-terminal
oec.tpl oxygen evolving complex
paa.tpl propionate A
pdd.tpl propionate D
PEH a phospholipid
TPO
PTR
PHO.tpl
PL9.tpl PL9
pqn.tpl
pro.tpl Proline
rsb.tpl
ser.tpl Serine
so4.tpl sulfate
thr.tpl Threonine
trp.tpl Tryptophan
tyf.tpl
tyr.tpl Tyrosine
ubq.tpl ubiquinone
UNK.tpl
UQ2.tpl quinone
val.tpl Valine

A table of topology files for Hemes

han five-coordinate b heme with one His ligand and one water/hydroxyl ligand
hcs five-coordinate c heme with one His ligand and one water/hydroxyl ligand
hce bis-his c type, esp charge
hcn bis-his c type, nbo charge
hcq his-met c type, charge from F. Autenrieth, J. Comp. Chem. 2004
hec his-met c type, hard charge
hmc bis-his c type, hard charge


A table of topology files for 1,4-Benzoquinone

The following applies to both Q and Q-

bzq unsubstituted BQ
2mb one-methyl BQ
23d 2,3-dimethyl BQ
25d 2,5-dimethyl BQ
26d 2,6-dimethyl BQ
tri trimethyl BQ
tet tetra-methyl BQ
tri trimethyl BQ (duroquinone)
26o 2,6-dimethoxy BQ
235 2,3-dimethoxy, 5-methyl BQ
556 2,3-dimethoxy, 5,6-dimethyl BQ

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
    • copy pdb file into it
    • copy run.prm into it
    • edit run.prm to input appropriate pdb
    • set step 1 to be true, steps 2-4 as false
  6. run MCCE (should take about 5-8 mins max)
  7. you should now have a bunch of new files. the important ones are called "step1_out.pdb" and "new.tpl"
    • from now on you are going to be modifying new.tpl
    • you need to assign orbital types to the atoms in the CONNECT part. the only orbital types supported are: s, sp, sp2, sp2, d2sp3
    • you need to add hydrogen atoms as appropriate
    • if you have multiple conformer types, each one needs its connectivity set up. for help with connectivity visit : http://xray.bmc.uu.se/hicup/
  8. 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
  9. move outfile to the parameter directory in your tpl directory
  10. delete new.tpl
  11. run MCCE steps 1-2 (set steps 1,2 to t in run.prm, steps 3,4 should still be f)
    • check for errors in run.log and debug.log.
    • fix errors and re-run MCCE until the errors no longer show up.

to add charges...

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

add radii

    • outside research required!!!


List of things to check

  1. All the conformations are made
  2. Connectivity is completed and correct
    • make sure everything is connected to the appropriate bits
  3. Use mk_iatom program to make CONFLIST, NATOM, IATOM entries
    • type : "mk_iatom filename (input) filename (output)"
  4. 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.
  5. check Proton and electron value for each conformer makes sense
    • go into the bit below the ATOMNAME and check out the proton and electron values, adjust as necessary
  6. Calculate the reference reaction field energy and put in as RXN entry
    • get the RXN entry from MCCE step 3

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