Note
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COMPARE¶
Description - `Procedure <#Procedure_>`__ - Analysis - Complete worked example (Zip file, 242 Kb)
Description¶
When COMPAREis present, a pair of protein systems is compared to
identify similarities and differences in their geometries. These systems
can be PDB or ENT files, MOPAC data sets, i.e., files that end in “.mop”
or “.dat”, or MOPAC archive files, i.e., files that end in “.arc”. The
comparison is done using a MOPAC data-set that contains information on
the locations of the systems to be used. A useful practice is to have
the systems in one or two folders and the data-set for the comparison in
another folder at the same level, e.g., if the systems are in
“Users/name/Crambin/Original PDB files” and “Users/name/Crambin/MOPAC
files” then the compare files should be in “/Users/name/Crambin/Compare”
In a normal run, atoms of one system are re-arranged to match those of the other system, so that both systems have the same atoms in the same sequence. The geometry of one system, “System A”, is then rotated and translated to minimize the difference between it and that of “System B.” Once the systems are in maximum coincidence, an analysis is performed; this identifies differences in the systems, differences in bond-lengths, and other quantities, such as the Root-Mean-Square and average atomic position differences.
If `LET <let.html>`__ is present, then hydrogen atoms that are
equivalent in the two systems, but have different names, will be treated
as if they were equivalent. Normally, these atoms would be excluded
from the analysis, but it’s useful to include them when different steps
in a reaction mechanism are being compared. This is particularly useful
when hydrogen atoms (protons or hydride ions) migrate from one atom to
another, for example when a hydroxyl group ionizes.
Procedure (General - Systems - Lines 2 and 3)¶
General¶
The recommended way to use COMPAREis to use a data set, e.g.
“compare the geometries of system-A and system-B.mop”, that contains
three lines of the type:
COMPARE geo_dat="System A" geo_ref="System B" output
Text to be displayed
Second line of text to be displayed (Optional)
In this form, with `OUTPUT <output.html>`__ present, the amount of
output is minimized and only data related to the comparison is printed.
A web-page in `HTML <HTML.html>`__, e.g., “compare the geometries of
system-A and system-B.html”, is written that allows a very rapid visual
comparison of features.
Systems¶
The text “System A” and “System B” should be replaced with the file-names for the systems of interest. For example, to compare a protein system “1A1A PDB structure.mop” and “1A1A optimized.arc” the first line would consist of:
COMPARE geo_dat="1A1A optimized.arc" geo_ref="1A1A PDB structure.mop" output
Compare original PDB structure and optimized geometry for system 1A1A
Do not use PDB files that are in the current directory - if they were to be used, then they would be over-written by the run. Instead, either re-name the file from <file>.pdb to <file>.ent, or have the PDB file in a different directory, and add the path or relative path to that directory, thus:
geo_ref="C:/Users/name/Original PDB files/1A1A.pdb (for Windows) or geo_ref="/Users/name/Original PDB files/1A1A.pdb" (for Linux)
or
geo_ref="../Original PDB files/1A1A.pdb"
Other keywords used¶
`NOSWAP <noswap.html>`__: By default, atoms can be swapped in the
`GEO_REF <geo_ref.html>`__ data-set if that would increase the
overlap with the `GEO_DAT <geo_dat.html>`__ data set. To prevent
this swapping, add NOSWAP.
NOREOR: Do not move the GEO_REF system to minimize the
difference between it and the GEO_DAT system.
`OUTPUT <output.html>`__: Not essential, but reduced the size of the
output, and allows the output of interest to be found more rapidly
Optional, but useful. This line will be displayed in the HTML web-page, and an informative description of the system can be very helpful later on when several web-pages are being used.
Lines 2 and 3¶
Optional. These lines will also be displayed in the HTML web-page.
Analysis¶
“Differences in atoms sets” - Self-explanatory. Have a quick look at the differences, and if nothing unexplained is seen, ignore this section.
“Number of atoms” - Self-explanatory.
“After docking - Atoms that move a lot” - This list is in order of decreasing motion. The first entry is the atom that shows the largest motion in going from one system to the other. A useful operation would be to open the HTML web-page generated by the run, and look at some of the atoms that move a lot.
“Residues that move a lot and their (Movement in Angstroms per atom)” - This list is in order of decreasing motion. The first entry is the residue that shows the largest motion in going from one system to the other.
In the next few entries, the assumption is made that one geometry is a reference, e.g., a PDB file downloaded from the internet, and the other is a geometry optimized using MOPAC.
In the HTML file, “Diff.” is the same as the “total” in the output file, and “RMSD” is the same as “RMS” in the output file.
“Differences between bond-lengths for the two geometries” - This is important. There are three common reasons for large (greater than 0.05 or 4%) differences in bond-length: (A) faults in the PDB structure, (B) faults in the computational method being used, e.g., PM7 with COSMO, and (C) incorrect hydrogenation resulting in a local fault in the chemical structure. To identify where the fault lies, examine the bond using the HTML web-page. In order to get a better view of the fault, display only the local environment of the two atoms. If the fault is identified as (A), ignore the fault - it was corrected by the geometry optimization. If (B), also ignore the fault, but make a note that this is a fault in the method being used, and might be important. If you think it is important, try using a different method, e.g., PM6-D3H4 with COSMO.
Most PDB structures do not include hydrogen atoms, and do not distinguish between the carboxylic acid C-O distances or between arginine CZ and (NH1 or NH2) distances. When a geometry is optimized, pairs of C-O and C-N bonds that PDB reports are the same length will be predicted to have distinctly different lengths, one will be a single bond and the other a double bond. This causes a difference in bond-lengths to be reported, but these differences are not a result of a fault in either the PDB or the semiempirical structure. Instead, these differences should be ignored. For example, the following Table lists the pairs of atoms that show the largest differences in bond-lengths. All the atom-pairs that involve carboxylate atoms, e.g. GLU CD and (OE1 or OE2), ASP CG and (OD1 or OD2) or guanidine atoms in ARG CZ and (NH1 or NH2) should be ignored.
Both PM6 and PM7 over-estimate the peptide C-N bond-length by about 0.08 Å, at about 1.37 instead of the expected 1.29 Å.
As a worked example, look at the Table
Table showing differences in bond-lengths between PDB and calculated geometries |
Differences between bond-lengths for
the two geometries
in GEO_DAT in GEO_REF
1 0.148 O(ATOM 524 OE2 GLU A 37) C(ATOM 52
3 CE1 HIS A 122) 1.404 1.324 |
Although this is a typical set of differences, every one of them falls into one or other of the types described above.
IMPORTANT: If the fault is caused by incorrect hydrogenation, than edit the optimized geometry to correct the fault, and re-run the geometry optimization. Then re-run the comparison to verify that the fault has been corrected. Incorrect hydrogenation most often occurs in substrates and hetero-groups such as heme rings. A lot of grief can be avoided by looking at differences in bond-lengths and checking for hydrogenation errors. For examples of PDB files that have severe errors in bond-lengths, see Preparing a starting data set.
Other global data such as the date, heats of formation, number of atoms, etc., are printed in the output and in the HTML web-page.