CAUTION:
The following notes are updated for PCMODEL version 7. However, there may still be some details in these notes that do not apply to this new verion. If you have any questions or suggestions concerning these notes, please contact the MolViz Facility Staff.

WARNING:
The QUERY function (measuring bond distances, etc.) in PCMODEL version 7 does not work. Also, the postscript output can be less than satisfactory in certain cases. We are working to find a solution to these problems.

NOTE:
To run the older version of PCMODEL, version 4.0, type pcmod4. This older version will be available until the new version is fixed.

• Starting the Program
• Drawing a Structure
• Interpreting Minimization Results
• Printing
• PC-MODEL Menus
  • INPUT menu
  • MINIM menu
  • DISPL menu

IMPORTANT!: Draw a SMALL portion of your structure and then minimize it. Then inspect your structure for correct stereochemistry, placement of hydrogens, etc. Fix your structure if necessary and reminimize. THEN add to your structure, and minimize/inspect again. If you try to completely draw a big structure and then minimize, it can be VERY difficult to fix problems.

The heat of formation (HF) is calculated using all atoms, or it is listed as INComplete. A notation indicates whether the calculation used dipole-dipole (DD) or charge-charge (QQ) electrostatic interactions. The MMX energy has a correction for 1-3 electrostatic interactions when two non-zero charged atoms are attached to a sp³ carbon. However, ir there are no cations or anions or no charged pi systems in a polar molecule, do a MMX-E calculation with DP-DP for more accurate energies.

If standard torsional potentials are NOT defined in MM2 for each torsion angle, the program will use generalized force field parameters which depend only upon the two central atoms. These generalized parameters are not optimal and energies produced with them should be considered accordingly (the geometries should be OK). Generalized parameters were used if the total energy is labeled MMX ENERGY; no generalized parameters were used if the total energy is labeled MM2 ENERGY.

The only circumstances where MMX energies may be compared directly is with conformers or diastereomers. A comparison of MMX energies for isomeric pi systems is invalid, because the potential energy of the pi system is NOT contained in the reported energy. A comparison of the heats of formation for all systems IS valid. The file pcmod.out lists details of the minimization results. See the PCMODEL manual for details about MMX, especially for transition states, metals, and other advanced modeling systems.

In the INPUT, MINIM, and DISPL menus, the READ, WRITE, and STOP options are always displayed. PCMODEL can READ and WRITE the following formats:

PCM	PCMODEL new file format
MMX	MMX standard file format
MM2	MM2(77) file format
MNDO	File format for molecular orbital program MNDO
MOPAC	Z-matrix form for MOPAC and AMPAC
X-RAY	generic x-ray file: header, cell parameters, X Y Z coordinates
MACROMODEL	MACROMODEL file format
SYBYL	file format for SYBYL (Tripos, Inc)
C3D	Chem3D format for Mac program Chem3D
PDB (READ only)	Protein Data Bank format
ALCHEMY (WRITE only)	Alchemy format

DRAW

See DRAWING A STRUCTURE

DELET

click on atoms and bonds to delete, then click on DONE

ADD-B

click on a bond to increase the bond order by 1. To draw a new bond, use DRAW.

UPDAT

updates the structure

H-A/D

first click on H-A/D deletes hydrogens not involved in hydrogen bonds, second click adds hydrogens according to a geometric perscription.

MOV-A

moves atom within the plane of the screen. Click on atom, then click at new location. Click UPDAT to show the atom in the new location. Then click H-A/D to quickly move hydrogens attached to atoms that you move.

M-IN

click on atom to move atom 0.5 angstroms into the plane of the screen.

M-OUT

click on atom to move atom 0.5 angstroms out of the plane of the screen.

ROT-S

use middle mouse button instead of ROT-S to rotate the entire structure. If a substructure is active, use ROT-S to rotate the substructure, and select FAST ROTATE

ERASE

erases a structure. First use WRITE to save the structure.

ROT-B

point to 4 atoms in dihedral angle---FIRST atom that you click on will move. Then click on slide bar (-45---0---+45) at top of draw box to smoothly rotate the angle. The farther you click on the edges of the slide bar, the faster you will rotate.

SSADD

reads previously stored structure file (in any format) into the program as a substructure

MAKSS

The substructure is created by pointing to an atom within an isolated structure, then to a blank spot in the drawing box. This will turn the entire isolated structure into a substructure. Or a portion of a structure can be identified as a substructure by first clicking on the "end" atom in the substructure followed by the the atom bonded to the "end" atom that is NOT in the substructure.

MOVSS

moves a substructure. Click on atom of substructure, then click on position to move atom. Entire substructure will then move.

CONEC

connects substructure to another structure. Both structures must have hydrogens. Click on a hydrogen in each structure; the hydrogens disappear and the bond will be made. The substructure will change orientation to make a reasonable bond.

S-VIS

sets a substructure to be invisable

BNDLB

changes the display to show bonds only, atom numbers, MMX atom types, substructure numbers and colors.

REDUC

shrinks size of structure

EPIMR

point to the center to be epimerized and then to the two attached atoms to be exchanged. Does not work if atoms are in a ring.

XY, XZ,ZY

view structure from XY, XZ, or YZ plane. Fast way to rotate the structure by 90°

RETYP

click on hydrogens that should NOT be removed by H-A/D (i.e., are non-volatile)

RESET

reinitializes options such as fixed atoms, pi atoms, atomic charge, etc. to default values.

H-BND

marks acidic hydrogens with a "~". Minimizations will recognize hydrogen bonding between these "~" hydrogens and other atoms.

PIATM

automatically or manually mark atoms in pi systems. To remove piatm designation, select PIATM and click on the atom.

COATM

coordinates metal with lone pairs or pi systems, and input charge on metal. Default metal charge = 0; setting a charge is NOT optimized---be cautious when interpreting results. If you do NOT use COATM, all metals are assumed saturated and NO attractive potential between metal and ligands.

FXDIS

prefered distances between atom pairs may be defined. Use a force constant ³ 50 mdyne/A to keep atoms fixed.

FXATM

fixed atoms will not move during minimization.

FXTOR

fixed torsion angles will not move during minimization

PRINT

generates postscript file for printing. See also PRINTING NOTES

CLIP

to zoom in on a region of the structure, point the mouse cursor in the center of the area to be expanded and click the left mouse button. To zoom out (make the structure smaller), click the right mouse button.

MMX-M

Performs a minimization. The atomic movement (in 10^-5 A) and energy (kcal/mol) are listed every 5 iterations. the program will periodically pause to check the effect of each atom's movement on energy. Type <esc> to terminate the minimization before reaching the final minimized state. See also Interpreting Minimization Results.

MMX-E

Computes energy, no minimization is performed

ROT-E

generates a graph of rotation energy barriers for acyclic torsion angle. The rotating parts are NOT minimized at each angle, but are held rigid. After displaying graph, you can return to origional angle or new angle. A more accurate barrier may be obtained by rotating to a maximum, performing MMX-M, and repeating ROT-E. See also D-DRV

BATCH

allows unattended processing of multiple structures in background (not shown on screen)

DOCK

performs a simulated annealing to minimize the energy between rigid structures by varying the position and orientation of the structures.

DYNAM

runs molecular dynamics simulations.

DCONT

continues molecular dynamics simulations

D-DRV

generates a graph of rotation energy barriers for acyclic torsion angle. The rotating parts ARE minimized at each angle. See also ROT-E. See also DIMAP.

DP-DP

uses bond dipoles for polar interaction term in electrostatic calculations (the origional MM2 protocol). Default = atomic charges (which is especially important for systems with charged atoms, e.g., N+ or C-)

BELOF

turns off the bell that rings when minimization is done

NAME

used to change the name of the structure in the program

PFLAG

sets level of detail of minimization info sent to the file pcmod.out

S-MIN

selects substructure to minimize

CONST

used to add your own constants to the minimization routine

ITERS

used to alter the number of minimization iterations. Default = 30,000

IT/S

used to alter the number of iterations to complete before pausing to ask if the minimization should continue. Default = 500

DIELC

set dielectric constant. Default = 1.5. If negative, then the dielectricis also multiplied by the interatomic distance, creating a "distance dependent" dielectric

Menu Items decribed under INPUT and PRINT

BNDLB

UPDAT

ROT-S

MOV-A

ROT-B

H-O/O

QUERY

STERO

AXY, AYZ, AXZ

redraws structure with 3 selected atoms in the specified plane

AX, AY, AZ

redraws structure with 2 selected atoms parallel to specified axis

BNDWD

increases bond widths

PAUSE

pauses program. Designed for PCs, not helpful on SGIs.

H-O/O

turns on/off display of hydrogens (hydrogens are STILL there)

R/S

click on four atoms arond common center in order of priority, then click in blank area of screen. R or S designation is displayed at blank area.

ENANT

click on atom, structure is reflected through Z axis (perpendicular to screen) at that atom.

QUERY

click on 1, 2, 3, or 4 atoms, then click on blank area of screen. The XYZ coordinates, distance, angle, or torsion angle (respectively) will be displayed. Click on UPDAT to clear the QUERY display.

PMR

click on two atoms, then at blank area of screen. Displays ¹H NMR coupling constants between 1,4 bonded protons in H-C-C-H chain (neither C can be a methyl group).

COMP

reads a previously saved structure into program and superimposes new structure on existing structure.

SURF

draw dot, CPK, space-filling, electrostatic, 3D surface. Can also generate postscript file of these surface drawings. See also PRINTING NOTES

ORTEP

draw ortep 3D surface. Can also generate postscript file of these surface drawings. See also PRINTING NOTES

EXPND

display PCMODEL window and structure without menus. Used to photograph screen. Type <Enter> to return to display & menus.

DIMAP

plots DIHED.XYZ (results from D-DRV in MINIM menu) or Weiler-type dihedral map of a ring

PEPTD

draws a ribbon through peptide backbone. Select "oxygen-oxygen" for smooth helical ribbons, choose "swapped orientation" for smooth sheet ribbons.

STERO

switches the display between stereo and mono

Menu Items decribed under INPUT Menu

ROT-S

PRINT

UPDAT

CLIP

BNDLB