pcgRUN requires Windows 95, Windows 98, Windows 2000 or Windows XP, PC GAMESS, and additional supporting software. You will need an editor, a builder, and a viewer to use with the program. See the below for options and downloading links for all these programs. I highly recommend Molekel as the visualizer.
| Type of Software | Some Free Software Packages for Academic Use | Source |
|---|---|---|
| The Interface | pcgRUN1.0 | http://jchemed.chem.wisc.edu/JCEWWW/Features/WebWare/collection/reviewed/index.html |
| PC GAMESS | PC GAMESS | http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml |
| File Editor | EditPadLite Notepad or WordPad can also be used. |
http://www.editpadlite.com/ |
| Structure Builder | ACD ChemSketch ISIS/Draw Accelrys ViewerLite |
http://www.acdlabs.com/download/chemsk.html http://www.mdli.com/downloads/free.html. http://www.accelrys.com/dstudio/ds_viewer/viewerlite/ |
| Visualizer | Molekel gOpenMol |
http://www.cscs.ch/molekel/ http://www.csc.fi/~laaksone/gopenmol/gopenmol.html2. Download and install PC GAMESS. |
(See the User Manual below for details and an example of how to do these.)
Windows Version
Wayne P. Anderson
Bloomsburg University and the MoleCVUE Project
pcgRun is a tcl/tk GUI to be used in conjunction with PC GAMESS 1. It allows one to build a molecule, save it, run PC GAMESS, and view the structure as a .pdb or .xyz file using free software that can be downloaded off the Internet. By using the resource file pcgRUN1.0rc.tcl, one can customize the interface to one’s own system. This is the first version of the program, and there is no guarantee that the program will work properly on your system. USE AT YOUR OWN RISK. Please report any bugs to wpa@bloomu.edu.
The Resource file
Many of the parameters in pcgRun can be set by the user in the resource file pcgrun1.0rc.tcl. This file is read immediately by pcgrun1.0.exe. It must reside in the same directory as pcgRun1.0.exe. The directories of the file editor, the browser, the builders, and the structure viewers must be specified in pcgrun1.0rc.tcl. Directories of the GAMESS executable, the input files and the output files must also be specified in pcgrun1.0c.tcl. Forward slashes (/) or double back slashes (\\) must be used to separate subdirectory specifications on Windows platforms. Thus, if the directory in which PC GAMESS resides is c:\gamess, “set gamessdir c:\\gamess” or “set gamessdir c:/gamess”. Four builders may be specified. Set the directory specifications for builder1 to builder4. Set the name to be associated with those builders as bld1nam to bld4nam. Similarly, four structure viewers can be specified. The directories are set as viewer1 to viewer4. The names of those viewers are specified as view1nam to view4nam. If the viewer is capable of reading an output file upon loading, vfile1, vfile2, vfile3 and vfile4 may be set to the value of the file extension, e.g. “pdb”. If they are set to “0", no file will be loaded when the viewer is opened. Note that Molekel does not recognize the “.out” extension as a GAMESS output file.
There are two files that initiate a PC GAMESS run. One is called “rungms1.bat” and the other “rungamess.exe”. Although each of them calls two programs - “gamess.exe” and “gamdone.exe”, “rungms1.bat” does not work in Windows 95 and on some Windows 98 and Windows Me systems. “Rungamess.exe” can be used on these systems, but it produces an extra window that has no function and can be annoying. Therefore, “set gamrun $gamessdir/rungms1.bat” first. If you get an error message saying the file cannot be found, then “set gamrun $gamessdir/rungamess.exe”. On Windows NT or Windows 2000 platforms, rungms1.bat must be used. The output will not be directed to gamess.out if rungamess.exe is employed.
.
Many of the programs mentioned in this manual have licensing restrictions. Be sure to consult the license agreements before using the programs.
Although any text file editor that can read large files can be used, the editor EditPad Lite® 2 has some very nice features, such as column editing and file conversion between UNIX and DOS or MAC and DOS, that are useful in dealing with input and output files. UltraEdit32® 3 is a relatively inexpensive shareware editor that has some additional nice features including the option of updating a file as changes are made. This makes it relatively easy to view changes in the output file using a couple of mouse clicks as PC GAMESS runs. To be safe, you should probably download a trial version and test its features before making a purchase.
Many of the default input parameters for PC GAMESS may be changed in pcgrun1.0rc.tcl as well. Unless the user is familiar with these parameters, it is probably best to stick with the default values.
Options in pcgRun1.0
BUILDER
The program used to draw and build the molecule is set in pcgrun1.0rc.tcl. Four builders may be set in the program. ChemSketch4 can be used to build a molecule in 2D and then convert the structure to 3D as long as a restricted subset of elements is present. One can use one of these elements to build a molecule initially, and then change to the desired element in the 3D structure. Only standard valences are supported by the 3D conversion utility in ChemSketch as well. The resulting structure can be saved in .mol format. ISIS/Draw5 can also be used to generate a 2D structure and save it in .mol format. The resulting .mol file can be read into ViewerLite™®6 and converted to 3D. If you use ViewerLite, be sure to turn on the 2D to 3D conversion option before importing the file from ISIS/Draw. If you also wish to use ViewerLite to view the final structure, be sure to turn the 2D to 3D conversion option off or your calculated structure will be altered upon import. Commercial programs such as HyperChem® 7 or PCModel®8 can be used as well. The builder must be able to generate an initial set of 3D coordinates for the molecule and be able to save the file in .mol format or in .pdb format.
VIEWER
Four viewers may be specified in pcgrun1.0rc.tcl. If the job is saved, the output structures will be converted to .pdb format with the name ‘jobname’.pdb and in .xyz format with the name ‘jobname’.xyz. pcgRun1.0 has been tested with gOpenMol9, VMD©10 and Molekel11, but other viewers may be used as well. Electron densities and molecular vibrations can be generated in Molekel or gOpenMol, although use of Molekel is more straightforward. Files for creating high quality Pov-Ray™12 ray-traced images can be generated in VMD. The gopenmol.bat file does not close down properly when it is started in pcgRun1.0. Therefore, the environmental variables in gopenmol.bat must be copied to the autoexec.bat file, and gopenmol.exe be called directly by pcgRun1.0. The executables and libraries of Molekel must be placed in the same directory as pcgRUN1.0.exe or be called by means of a .bat file for Molekel to be accessed from pcgRUN1.0.exe.
JOB Name
The name of the JOB must be entered here. The files ‘jobname’.out, ‘jobname’.pdb, ‘jobname’.dat, and ‘jobname’.xyz will be generated in the output directory if the job is saved. The input coordinate file must also have the name ‘jobname’.xxx as specified below. If an IR spectrum is generated, an additional file, ‘jobname’.vir, containing the simulated ir spectrum is also placed in the output directory.
BUILD
The BUILD button calls up the builder specified above. The molecule must be converted to 3D and saved as ‘jobname’.mol, ‘jobname’.ent, ‘jobname’.pdb, ‘jobname’.xyz, or ‘jobname’.mcm in the input directory specified in pcgrun1.0rc.tcl. A previous GAMESS output file, named ‘jobname’.out, may also be copied to the input directory and used as input. If the input and output directories are the same and the input file is in .pdb, .xyz or .ent format, a copy of the input file ‘jobname.pdb’, ‘jobname’.xyz or ‘jobname’.ent is saved as ‘jobname’.in.pdb, ‘jobname’.in.xyz or ‘jobname’.in.ent since ‘jobname’.pdb, ‘jobname’.xyz or ‘jobname’.ent will be overwritten by the output file. It is best to have separate directories for input files and output files.
GAMESS INPUT
The GAMESS INPUT button allows one to set many of the input parameters for PC GAMESS. In many cases the default parameters will work. At a minimum the RUNTYP, BASIS, and INPUT FILE type will have to be set for each run. The coordinate input file must be in the input directory specified in pcgRUN1.0rc.tcl.
Some of the options require additional input that cannot be entered through pcgRun1.0. It is the responsibility of the user to review the input file generated by pcgRun1.0 and make any additions or changes that are necessary for a successful run. I cannot guarantee that the settings that are placed in the input file will necessarily give a meaningful run. Be sure to read the GAMESS documentation files, particularly INPUT.DOC. If a copy of INPUT.DOC is placed in the same directory as PC GAMESS, it can be accessed from the HELP menu of pcgRUN1.0.
Summary of GAMESS INPUT Options
(Items in bold are the ones that are changed most often.)
INPUT COORDINATE TYPE |
NONE |
The coordinates are to be entered manually by the user. |
|
mol |
Coordinates are to be read from a file in “mol” format named ‘jobname’.mol |
|
pdb |
Coordinates are to be read from a file in “pdb” format named ‘jobname’.pdb |
|
ent |
Coordinates are to be read from a file in HyperChem “ent” format named ‘jobname’.ent |
|
xyz |
Coordinates are to be read from a file in “xyz” format named ‘jobname’.xyz |
|
mcm |
Coordinates are to be read from a file in Calleo “mcm” format named ‘jobname’.mcm |
|
out |
Coordinates are to be read from a GAMESS output file named ‘jobname’.out. |
GROUP |
|
Indicates the point group that is to be used to build the molecule from symmetry unique coordinates. If the coordinates of all atoms are specified as input, choose C1 as the point group. |
NAXIS |
|
Indicates the the order of the principal axis when the point group specification includes an “N”. |
$CONTRL
EXETYP |
CHECK |
Indicates that the input file is to be checked for errors. |
|
RUN |
Indicates that a full GAMESS run is to be done. |
RUNTYP |
ENERGY |
A single point calculation is to be done at the geometry specified in the input file. |
|
OPTIMIZE |
The geometry of the molecule is to be optimized |
|
HESSIAN |
The force constants and vibrational frequencies are to be calculated at the geometry specified in the input file. |
|
SADPOINT |
A transition state calculation is to be done. |
|
IRC |
An intrinsic reaction coordinate calculation is to be run. |
|
PROP |
Certain specified properties of the molecule at the geometry specified in the input file are to be calculated. This requires some manual editing of the file. |
SCFTYP |
RHF |
A restricted Hartree Fock calculation is to be carried out. This option is used for closed shell systems. |
|
UHF |
An unrestricted Hartree Fock calculation is to be carried out. This option is generally used for systems containing unpaired electrons. |
|
ROHF |
A restricted open shell Hartree Fock calculation is to be carried out. This option is sometimes employed for systems containing unpaired electrons. |
MPLEVL |
0 |
No MP2 calculation is to be carried out. |
|
2,3,4 |
Electron correlation is included through an MP2, MP3 or MP4 perturbation theory calculation following the Hartree Fock calculation. |
ICHARG |
Specifies the overall charge on the system. |
MULT |
Specifies the multiplicity of the system. This equals n+1, where n is the number of unpaired electrons. |
ECP |
NONE |
Effective core potentials (pseudopotentials) are not being used. |
|
SBK |
Use the Stevens, Basch, Krauss, Jasien, Cundari ECP’s for the core electrons. |
|
HW |
Use the Hayes-Wadt ECP’s for the core electrons. |
|
READ |
The ECP’s are to be specified in the input file. This option requires manual editing of the input file. |
MAXIT |
The maximum number of iterations that are permitted to achieve SCF convergence. |
COORD |
CART |
The atom positions are expressed in Cartesian coordinates. This option must be used if the molecule is built with the BUILDER in pcgRun. |
|
UNIQUE |
See GAMESS manual. |
|
ZMAT |
The coordinates are expressed in the form of a Z-matrix. The coordinates must be supplied manually if this option is selected. |
$SYSTEM
TIMLIM |
This gives the maximum time in minutes allowed for the run. |
MEMORY |
This gives the maximum number of words of memory allowed for the run. Large jobs will require a larger number than the default. |
$BASIS
GBASIS: NGAUS |
These options are used to specify the basis set. To indicate STO-3G, set GBASIS to STO and NGAUS to 3. For 3-21G, set GBASIS to N21 and NGAUS to 3. For 6-31G, set GBASIS to N31 and NGAUS to 6. Several additional basis set options, including those for use with ECP’s, are given as well. See the GAMESS documentation. |
NDFUNC |
Gives the number of sets of d polarization functions to be added to the heavy atoms. For 6-31G(d), which is often designated as 6-31G*, and for 6-31G(d,p), which is often called 6-31G**, NDFUNC=1. |
NPFUNC |
The number of sets of p polarization functions to be added to hydrogen atoms. For 6-31G(d,p), NPFUNC=1. |
DIFFSP |
.TRUE. .FALSE. |
A diffuse sp function is included on non-hydrogen atoms in the basis set. This is often used with anions and is designated with a + in the basis set specification. For 6-31+G(d,p), DIFFSP=.TRUE.. |
DIFFS |
.TRUE. .FALSE. |
A diffuse s function is included on hydrogen atoms in the basis set. This is often used with anions and is designated with a + in the basis set specification. For 6-31++G(d,p), DIFFSP=.TRUE.. |
$SCF
DAMP |
.TRUE. .FALSE. |
Set to .TRUE. to help prevent oscillations in the energy during SCF iterations. This is often necessary with transition metal complexes. |
SHIFT |
.TRUE. .FALSE. |
Set to .TRUE. to shift the energies of the virtual orbitals to assist convergence during SCF iterations. This is often necessary with transition metal complexes. |
$STATPT
HSSEND |
.TRUE. .FALSE. |
If set to .TRUE., the force constants and vibrational frequencies are calculated at the end of a geometry optimization. |
NSTEP |
Indicates the maximum number of cycles allowed in a geometry optimization |
ADVANCED OPTIONS
Generally these parameters do not have to be changed. However, they permit additional control over the calculation.
$CONTRL
.
MOLPLT
|
.TRUE .FALSE. |
Specifies whether the final coordinates are to be saved in Molplot format in ‘jobname’.dat. |
AIMPAC |
.TRUE. .FALSE. |
Specifies whether information for a Bader Atoms in Molecules input file is saved. |
INTTYP |
POPLE HONDO |
Indicates whether Pople or Hondo integrals are used. See GAMESS documentation. |
$BASIS
NFFUNC |
The number of sets of f polarization functions to be added. |
$GUESS
GUESS |
HUCKEL |
Indicates that a Huckel approximation is to be used to generate the initial MO wavefunctions |
|
MOREAD |
Indicates that the MO’s are to br read from a previous calculation. This requires additional input. |
NORB |
Indicates the number of MO’s to be read when GUESS=MOREAD. See the GAMESS documentation. |
$SCF
NCONV |
Gives the SCF convergence limited as 10-n. |
DIRSCF |
.TRUE. .FALSE. |
Indicates whether a direct SCF calculation is to be carried out |
$STATPT
OPTTOL |
Gives the gradient convergence tolerance in Hartree/Bohr. If this value is changed, the value of NCONV will also have to be adjusted. |
HESS |
GUESS |
Chooses a positive definite diagonal Hessian as an initial; guess |
|
READ |
Reads the Hessian from $HESS. Additional data must be supplied manually. |
|
CALC |
The initial Hessian is computed. See $FORCE. Additional input may be required. |
$CUBE
CUBE |
.TRUE. .FALSE. |
PC GAMESS allows one to generate cube files for displaying electron densities in gOpenMol. If CUBE=.TRUE. the cube file is generated if IEDEN is set to 1 in $ELDENS. |
MESH |
COARSE MEDIUM FINE |
This gives the size of the grid used in the cube file. A COARSE grid is generally sufficient. MEDIUM and FINE grids will generate very large cube files. |
$ELDENS
IEDEN |
0 |
Electron density is not computed |
|
1 |
Electron density is computed |
MORB |
Indicates the MO whose electron density is to be computed. If this is set at 0, the total electron density is computed. Otherwise, the MO number must be entered. |
$ELPOT
IEPOT |
0 |
The molecular electrostatic potential is not computed. |
|
1 |
The molecular electrostatic potential is computed. If CUBE=.TRUE., IEDEN=1, and IEPOT=1, a cube will be produced for both the electron density and the ESP. This allows one to plot the ESP on the total electron density surface using gOpenMol. |
APPLY
The input file is written with the specified parameters. Until this button is pushed, no change is made in any previous input file.
VIEW INPUT FILE
The VIEW INPUT FILE button calls up the required PC GAMESS input file “input” for viewing. The “title” of the run and any special parameters can then be set manually.
RUN
The RUN button calls “rungms1.bat” or “rungamess.exe” to start a PC GAMESS run. The program “gamdone.exe” is called at the end of the run to call up a window indicating that the GAMESS job is finished.
VIEW OUTPUT FILE
The VIEW OUTPUT FILE button calls up the editor to read the file gamess.out at the end of the run.
SAVE JOB
The SAVE JOB button generates two files, ‘jobname’.pdb, and 'jobname'.xyz from the last set of coordinates in the PC GAMESS run. These files are saved in the output directory. In a geometry optimization, if the equilibrium geometry is not found during the run, ‘jobname’.pdb or 'jobname'.out can be moved to the input directory and used to generate a new input file. In addition the GAMESS output file, gamess.out, and the PUNCH file, ‘jobname’.dat, are copied to the output directory as ‘jobname’.out and ‘jobname’.dat.
VIEW STRUCTURE
The VIEW STRUCTURE button calls up the specified viewer. If vfile is set to “pdb" for that viewer, the output structure ‘jobname’.pdb is read into the viewer immediately. If vfile is set to “0" in pcgrun1.0rc.tcl, the viewer is called up, but the user must select the file manually.
GENERATE IR SPECTRUM
The GENERATE IR SPECTRUM button generates a file irspectrum.dat that contains the calculated frequencies and intensities for visualization. A Lorentzian peak is built around each of the calculated frequencies to simulate the spectrum. The job must be saved prior to generating the IR spectrum because 'jobname'.out and 'jobname'.dat are read from the output file. Irspectrum.dat is copied to the output directory as 'jobname'.vir following the generation of the IR spectrum. Also, a HyperChem script file, ‘jobname’.scr, is created in the output directory. This file can be used to animate the vibrations in HyperChem.
VIEW IR SPECTRUM
The VIEW IR SPECTRUM button calls up a TCL/TK IR spectrum visualizer utilizing irspectrum.dat as input.
References
1. PC GAMESS
PC GAMESS is an functionally extended version of GAMESS(US), an ab initio quantum mechanical package. The leading developer of PC GAMESS is Alex A. Granovsky, Laboratory of Chemical Cybernetics at Moscow State University (MSU). The General Atomic and Molecular Electronic Structure System (GAMESS) is maintained by the Gordon research group at Iowa State University.
http://quantum-2.chem.msu.ru/gran/gamess/index.html
http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml
2. EditPad Lite®
3. UltraEdit®
4. ACD/ChemSketch© Freeware
http://www.acdlabs.com/download/chemsk.html
5. ISIS/Draw™
6. ViewerLite™
http://www.accelrys.com/download/
7. HyperChem®
8. PCModel®
http://serenasoft.com/index.html
9. gOpenMol
gOpenMol is maintained by Leif Laaksonen, Center for Scientific Computing, Espoo, Finland.
http://www.csc.fi/~laaksone/gopenmol/gopenmol.html
10. VMD©
VMD was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.
See Humphrey, W., Dalke, A. and Schulten, K., ``VMD - Visual Molecular Dynamics'' J. Molec. Graphics 1996, 14.1, 33-38.
11. Molekel