Comqum-X

The following contains a short guideline to the software developed by Ulf Ryde for solving protein crystal structures guided by QM/MM energies. A more exhaustive guideline can be found at Ulf Ryde's personal homepage; http://signe.teokem.lu.se/~ulf/Methods/comqum\_x.html

1. First, we need a refined crystal structure (pdb file) including structure factors (CVS file). Both can be downloaded from the pdb data base http://www.rcsb.org
2. Copy needed files cp /lunarc/nobackup/projects/bio/Data/Comqumx\_lib/\* .
	1. Modify the sedfile (see example below) and specify the source of coordinates (usually the pbd file - this can optionally be renamed e.g. to coord\_pdb\_id).
3. pdb data (see http://signe.teokem.lu.se/~ulf/Methods/comqum\_x.html)
4. Alternate configurations. Delete (keep highest) or include; can be done by maestro or by changepdb, command occ. A good check if occupations are deleted is to take the major occupation and see if Rfree changes
5. Insert END at the end of all files (we did not do this?)
6. Do changepdb, command seg followed by w (formatting)
7. get topology files for unusual residues (many can be found at the HIC-UP server)
8. Continue from here..... (NOT DONE YET)
9. Run cqx\_sedscript; this will construct the CNS files "bindividual.inp  bindividual1.inp  generate.inp  make\_cv.inp  mmrun2  mmrun3". The b-individual files contain information about the B-factors from the crystallographic data.
10. run generate.inp
 cns <generate.inp >generate.out

grep ERR generate.out

grep WRN generate.out

grep INFO generate.out

grep error generate.out

grep warning generate.out
Note; if there are alternate configurations in the coordinate pdb file given in the CNS format (look for AAC1 or BAC1 in the coordinate pdb file), these have to be deleted by vi-editor command:
:%s/AAC1/B /g

:%s/BAC1/B /g
Note that the lowest points 10. - 12. in Ulf's guide are not required configurations
11. run pdbtocomqum: Select system 2 as 1000.0 and system 3 as 0.0
Note: When running an X-ray with hydrogens, the control file contains $pointcharges. This should be deleted!
12. Cont. list

## sedfile example

s/cqx\_space\_group/p2(1)2(1)2(1)/ # Change! Look for SPACE GROUP

s/cqx\_crystal\_alpha/90/ # Default, check: Look for CRYST1 (unit cell dimension; angles)

s/cqx\_crystal\_beta/90/

s/cqx\_crystal\_gamma/90/

# Look for CRYST1 (unit cell dimension; lenghts)

s/cqx\_crystal\_a/32.040/ # Change! Look for CRYST1 (unit cell dimension; lenghts)

s/cqx\_crystal\_b/75.560/

s/cqx\_crystal\_c/120.360/

s/cqx\_coord\_file/lpmo\_5vg0\_coord/ # rename pdb file to this name

# Find these under "Dictonaries" at HIC-UP server ("CNS/topology files and CNS parameter files")

s/cqx\_top\_file1/per.top/

s/cqx\_top\_file2//

s/cqx\_top\_file3//

s/cqx\_par\_file1/per.par/

s/cqx\_par\_file2//

s/cqx\_par\_file3//

# Reflections file

s/cqx\_reflex\_file/lpmo\_5vg0.cv/ # Change this one!

s/cqx\_test\_percent/1.72/ # Change: Look for FREE R VALUE TEST SET SIZE under FIT TO DATA USED IN REFINEMENT.

s/cqx\_resolution\_up/32.0/ # Change: Look for RESOLUTION RANGE LOW under FIT TO DATA USED IN REFINEMENT.

s/cqx\_resolution/1.10/

s/cqx\_map\_residues/(resid 1) or (resid 2)/