Note that you need to use a special, modified version of phenix (to write out energies and gradients): /lunarc/nobackup/projects/snic2019-35-66/Octav/TestPhenix/Phenix/phenix-1.14-3260
1.Start
with
a refined crystal structure, including structure factors (i.e. the pdb
file and a structure factor file in cif format, downloaded from https://www.rcsb.org).
Convert
the structure factors from cif to mtz using
Both these steps are conveniently done by phenix.fetch_pdb --mtz pdb_id
Alternatively, if you already have downloaded the pdb and cif files, you can do: phenix.cif_as_mtz cif_file
space
group (as in the CRYST1 entry in the PDB file)
unit
cell information (as in the CRYST1 entry in the PDB file)
PDB
file name: default pdb3
X-ray
MTZ file name
Neutron
MTZ file name: enter “None” if no neutron refinement
Reflection
labels
(from reflection file editor in Phenix; i.e. run phenix, select
Reflection tools and then Reflection file editor; then Add file; then
read Array label of Amplitude and R-free flag (for the next point) or
run sftools then READ and give the mtz file name; look for types F and Q
(and I for ); the default "FOBS,SIGFOBS" are often correct
R-free
labels (as above; the default "R-free-flags" is often correct)
Non-standard parameter (cif) files, if any.
Then, run sed -i -f sedfile2 mmrun2
5.Delete
alternative conformations in the quantum system. Other alternative
conformations can be kept.
6.Protonate
the quantum system (for example, using phenix.ReadySet). The rest of the
protein can also be fully protonated, the hydrogen atoms will be kept riding.
7.Run
pdbtocomqum
Select the name of the log file
(default is OK)
Enter the name of the pdb file
(comqum.pdb)
Do not search for short contatcts
Enter a new title (is normally done in the
file in next point).
Select the quantum system, including
the junction atoms that will be changed to hydrogens (you first give the number
of the amino acid, then the number of the atoms in this amino acid; one
<CR> let you select a new amino acid; another <CR> ends the
selection).
This is better done by entering the name of a file with the atom
numbers (see below). This file should also contain the new title as the first
line.
0 water molecules to include
Enter 1000 A (everything is included)
There is no
need to include or remove residues from this system (hit return twice).
Enter 0 Å (the whole protein has already been
included).
Select a phenix type of calculation
by typing p, or h if hydrogens should be included (neutron data).
Select the basis set (i.e. the type
of junction, typically 12).
Press return until the program is finished
8.Run comqumtoturbo to get the Turbomole files: control
coord
9.Check the name of metal atoms in
file coord and then run define
construct an UFF hessian in the geometry menu
define the basis sets
get starting orbitals
possibly change the DFT functional
turn on the ri calculations
turn on DFT-D4 or D3(bj) dispersion
10.Run one test refinement to get
parameters for the junctions
phenix.refine
mmrun2 > mmrun2.out
mv
mmrun2_1.geo mm2.geo
mv
mmrun2_1.pdb pdb3
You may need to set
disable_suitability_test = True.
RuntimeError: No data for scale calculation.
Means that there are no selection of reflections for Rfree.
11.Run
comqumtophenix ! This does not work for the moment
This will generate or change the following files: pdb1,
junc.cif and comqum.dat
12.Edit
sedfile1, with the residues in the quantum system, with the syntax “resseq x
and chain A or resseq y and chain B or…” and the ligand parameter file (if
the ligand is in the quantum system; otherwise None)
13.Run
sed -i -f sedfile1 mmrun1
14.Test
mmrun1 by running
phenix.geometry_minimization mmrun1 > mmrun1.out
15.You should
always run with a fixed value of the weight factor (even if you want the
default one). This is done in the file mmrun2 (search for fix_wxc = ). Run fixenergy_phenixin to get the
default value of weight (take the first in the output of this program - there
are two). ! I have not done this
16.Remove unneccesary files and make a
backup by running cqxbackThis also needs to be changed
The following 19 (20 for UHF) files are needed to run comqumx: basis
control
grad1
mm1.pdb1
mm3.pdb1
junc.cif mmrun2
coord
mmrun1 mos comqum.dat
bindividual
In addition, you need the structure factor file and the parameter
files for all heterocompounds.
17.You can add restraints on a distance
between two atoms using (note the unusual units):
$restraints
atom1(1) atom2(1) desired_distance_in_A
force_constant_in_au
$restraints
1 3 1.00 1.0
A typical force constant is 1 a.u. (which typically gives less than 0.01 �
deviation at convergence)
18.Start comqumx:
comqumx-phenix -c 200.
The results are in files energy and cns.dat.
The final coordinates are in bindividual_1.pdb and
coord
Extra info
To run the phenix properly, you have to modify two files
in Phenix (Search for ComQum):
Weights and r/rfree for neutron data
are currently not printed but easy to find in minimization.py
Some inspiration about the cif files can be obtained from:
/lunarc/nobackup/projects/snic2019-35-66/Octav/TestPhenix/Phenix/phenix-1.14-3260/modules/elbow/elbow/chemistry/CIF_formats.py
It gives cif lines and atom types.
For torsions, you have three options:
CONST – for harmonic, with period 0 ; they need to be CONST_01, CONST_02 and so on
Var – for sinusoidal, with period >0; they need to be Var_01, Var_02 and so on
chir – for impropers, similarly chir_01, chir_02 and so on
comqumtophenix should:
read
a geo file from refinement
extract
parameters for all the bonds/angles/dihedrals/improper involving junction atoms
and atoms in the quantum system and scale bond parameters according to the
junction factors
write
a cif file with modifications for the residues containing junction atoms;
impropers are written as dihedrals with a harmonic potential (i.e. 0 in the
period)
write
pdb1 from comqum.mmout
eventually
extract point charges but I have not found them yet