Notes on Proteins

(All solids - Periodic Table - Home - Manual - PM7 Proteins - PM6-D3H4 Proteins)

General

  Proteins were selected to include a wide range of types.  These cover: simple proteins, such as crambin and barnase; metalloproteins, e.g., myoglobin, and calmodulin; oligomeric proteins, e.g., hemoglobin and the potassium channel; and polymeric proteins such as silk and a collagen-like protein. The purpose of the tables of proteins is to show how to specify various types of proteins.  The proteins are not intended to be used directly for modeling experiments.  No checks have been done to ensure that the starting structures are chemically sensible.  The suggested check - to verify that all charged sites are valid - has not been carried out.

Layout of the PM7 and PM6-D3H4 Proteins tables

No.: Proteins are listed in alphabetical order.  The number only indicates where each protein is in that list.

Protein: All files for each protein is identified by a name.  This typically consists of the name of the protein in the PDB and a four-digit name assigned by the PDB. If the name is also a hyperlink, then the "Specific Script" will be active.  This will replace the default image of the protein with a feature of that specific protein.

No. atoms: The total number of atoms in each system.  This includes hydrogen atoms, and all small molecules such as water, ligands etc. that are present in each system.

PDB:
Δ
Hf:
 Proteins from the PDB often lack hydrogen atoms.  These have been added and their positions optimized, during this process, some salt bridges may form. The heat of formation represents the protein with the positions of the hydrogen atoms optimized. This is the starting geometry.  Jmol: A Jmol picture of the type generated by MOPAC when keyword HTML is used.
ARC: The contents of the ARC file for the protein will be downloaded.  This can be copied to a local folder.
PDB: The contents of the PDB file for the protein will be downloaded.  This can be copied to a local folder.

10 Kcal/2 constraint:
The starting geometry is allowed to relax slightly, i.e., all geometric variables were optimized, but a restraint was imposed that imposed a penalty of 10 kcal mol-1 for every Ångstrom2 an atom moves from its original position.
ΔHf:  The heat of formation, in kcal mol-1, of the system. This does not include the energy from the restraining function.
RMS: The average motion is the average movement in Ångstroms of each atom relative to the starting geometry.
Jmol
:
A Jmol picture of the type generated by MOPAC when keyword HTML is used.
ARC: The contents of the ARC file for the protein will be downloaded.  This can be copied to a local folder.
PDB: The contents of the PDB file for the protein will be downloaded.  This can be copied to a local folder.

3 Kcal/2 constraint:
This is similar to the 10 Kcal/2 constraint , but with the restraining function replaced with 3 kcal mol-1 Å-2.
ΔHf:
 The heat of formation, in kcal mol-1, of the system. This does not include the energy from the restraining function.
RMS:
The average motion is the average movement in Ångstroms of each atom relative to the starting geometry.
Jmol
:
A Jmol picture of the type generated by MOPAC when keyword HTML is used.
ARC: The contents of the ARC file for the protein will be downloaded.  This can be copied to a local folder.
PDB: The contents of the PDB file for the protein will be downloaded.  This can be copied to a local folder.

Unconstrained:
ΔHf:
 The heat of formation, in kcal mol-1, of the unconstrained system.
RMS:
The average motion is the average movement in Ångstroms of each atom relative to the starting geometry.
Jmol
:
A Jmol picture of the type generated by MOPAC when keyword HTML is used.
ARC: The contents of the ARC file for the protein will be downloaded.  This can be copied to a local folder.
PDB: The contents of the PDB file for the protein will be downloaded.  This can be copied to a local folder.

Statistics:

At the bottom of the tables there are average Root-Mean-Square errors in Ångstroms for the biased and unbiased optimizations.  The reference geometries are the hydrogenated PDB systems.