How to convert an existing mcce tpl file to free format tpl file?¶
Page last updated on: 2020-07-07
There accumulated a big number of mcce tpl files (topology file of a molecule) which defines the conformers, atoms, connectivity and so on. Since mcce tpl file follows strict format, new mcce adopted a free format to save the same information. Follow these steps to convert an existing mcce tpl file to a new free format tpl file.
This example is assuming you convert a mcce tpl file glu.tpl in param04 directory.
Convert¶
Run this command to convert mcce format to free format.
$ bin/tpl-mcce2free.py param04/glu.tpl > glu.ftpl
The above output file has most entries converted.
Fix "rxn" record¶
Then we can manually compile rxn values in CONFORMER records. First manually replace rxn= with rxn02=, rxn04=, rxn08= depending on the dielectric constant of the tpl file that was converted from.
CONFORMER, GLU01: Em0= 0.0, pKa0= 0.00, ne= 0, nH= 0, rxn02= -6.410, rxn04= -3.100, rxn08= -1.390
Error check¶
Now find the atom name difference, especially H atoms. PDB is using version 3 names and old mcce is using version 2 names. For GLU, the name comparison can be found at here.
If you have a pdb file of the residue/ligand, we can test the ftpl file against that pdb file:
$ bin/verify_tpl.py ftplfile pdbfile
It will report any atoms that can not be loaded by the converted ftpl file definition.
To change the name in ftpl file, glu.ftp for example:
$ sed -i 's/1HB / HB2/g' glu.ftpl
You can verify the ftpl file again after the change of names.
Store in param directory¶
Finally, place the tested ftpl file under MCCE distribution's "param" directory.
The MCCE distribution directory is the (HOME) line in your run.prm.