HyperChem Release 7.x 

Frequently Asked Questions

Please select the topic you are interested in:

HyperChem - Snapshot files
HyperChem - Tutorials
HyperChem - Constrains & Restraints
HyperChem - Ab initio disk space
HyperChem - Drawing Using Formal Charges
HyperChem - Citation
HyperChem - File Formats
HyperChem - Viewer Rotation
HyperChem - Unknown MM Parameters
HyperChem - Zero Point Vibrational Energy
HyperChem - Aligning NH3
HyperChem - Heats of Formation
HyperChem - DFT using 5 or 6 d-orbitals
HyperChem - Ab Initio Optimization of Excited States
HyperChem - Newton.exe crashes under Windows XP

HyperChem - Snapshot files

HyperChem allows you to run a Molecular Dynamics simulation and compute/plot the averages of the parameters used or to save the simulation in a Molecular Dynamics snapshots (SNP) file.  This file will contain all the information of the simulation and will allow you to extract information or playback the simulation later.

Snapshots files are only playable by opening the associated HIN file and select Playback from the Molecular Dynamics dialog box. This will allow you to view a portion or the entire dynamics simulation. 

The snapshot file is in binary form to save disk space, but there is a utility available from our site that will convert it to text form. The Snap2text utility is available from www.hyper.com/support/ by selecting Downloads and then HyperChem Utilities and browsing to the Snap2text utility. 

HyperChem also has the functionality to make an AVI movie from a snapshot file, so you could simply use any media player to show a dynamics simulation. Select Playback and enable Create Movie in the Snapshot options to create the AVI file.



HyperChem - Tutorials

The HyperChem 7.5 and HyperChem 7.1 CD's include about 240 MB of tutorials, but due to the size, these are not available for download. Sample tutorials are available at the link below. Contact sales@hyper.com for a HyperChem Evaluation CD to get the tutorials.

Sample Tutorials Available Here



HyperChem - Constrains & Restraints

There is a difference in using constrains and using restraints. Constraints are used for building the molecule to a specific structure, but allowing optimizations and dynamics to go from there. Restraints are spring forces that hold atoms, bonds or torsions to a specific value. What you want is to use a restraint with a high force constant.

To use restraints, first select the atoms you want to constrain and name the selection. The use the Setup->Restraints dialog to choose the named selection and add the value and force constant you want to use.



HyperChem - Ab initio disk space

ERROR: Trouble in writing 2e integrals to file C:\Temp\stempfile.; please check your disk space.

This means that the ab initio integrals HyperChem stored on disk have consumed all available space on the drive. You must use a smaller basis set, smaller molecular system, free up some disk space or use a drive with more disk space.

The location where ab initio integrals are stored to disk is specified in the Preferences dialog box (File->Preferences->Paths->Ab initio integrals). You may set this location to any folder on any drive. Choose the one with the most available disk space. Ab initio integrals for large systems can take up many GB of space. The default location for ab initio integral files is the current user temporary file location set in Windows.

When the error appears, the temporary integral file will be erased, so it'll appear that there's lots of free space.



HyperChem - Drawing Using Formal Charges

A few important rules about building molecules that don't obey the 'simple' rules:

1. You may add more bonds than allowed by selecting 'Allow Arbitrary Valence' from the Build menu. This will allow you to add a triple bond to oxygen.

2. The Model Builder, by default, follows the rules. This means that you have to delete hyrdogens that have been added or use the Set Formal Charge.

3. Using Build->Set Formal Charge will tell the Model Builder to not add hydrogens.



HyperChem - Citation

HyperChem(TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA

HyperChem - File Formats

HyperChem Professional Release 7 supported file types: 

	*.hin	HyperChem files
	*.ent	Brookhaven PDB files
	*.skc	ISIS Sketch files
	*.xyz	Cartesian files
	*.mol	MDL MOL files
	*.zmt	MOPAC Z-Matrix files
	*.ml2	Tripos MOL2 files
	*.chm	ChemDraw CHM files (Input only)

HyperChem - Viewer Rotation:
In HyperChem, if you want the molecule to move rather than the viewer, you have it selected and use the right button. Also, the viewer should be looking down the z axis (align viewer) to make easy sense of the molecule on the screen and its true molecular coordinates. Also you have to know that you can perform operations with a subset selection and the various align operations will align the selection rather than the molecule. The rest of the molecule will move along with the alignment if you have whole molecule translation invoked (Preferences/tools menu). 

The important thing here is that if you understand how HyperChem treats the viewer and the molecule transformations separately then this is pretty easy. That is you need to know how to translate and align a molecule not just yourself the viewer.

HyperChem - Unknown MM Parameters:
I have tried to draw a gold surface and calculates its energy with MM and amber. Then, I found that the atom type for gold is unknown (**) for both force field. However, HyperChem gives the single-point energy for MM but not amber. Why? Where can I look for or change the parameter?

The MM+ force field has default parameters based on position in the periodic table and simple hybridization rules when there are no known parameters. These parameters are essentially the ** force field (universal force field) and are described in the manuals but are not adjustable in a text file like the remaining HyperChem parameters. It is not expected that this default set is particularly accurate compared to hypothetical "specifically derived" parameters for gold. Unfortunately gold is far enough down the periodic table that theoretical chemistry hasn't as much to say about it as other elements.

You could, however, add parameters for gold to any of the other force fields -- amber, charmm, MM+ etc. by adding values to the parameter text files if you know values you think would be better than the default values.

All these issues are discussed in the manuals at various places. Although adding parameters is relatively easy, it may require a little experience with molecular mechanics ala HyperChem style.

The default force field is there with Amber and Charmm, as well, in later versions of HyperChem so you must have a relatively older version of HyperChem.

HyperChem - Zero Point Vibrational Energy:
Zero Point Vibrational Energy (ZPVE) is just a simple function of the vibrational frequencies so a simple script could add up the ZPVE (0.5hv0) for each frequency from a vibrational analysis. 

HyperChem - Aligning NH3 Example:
If you have random ammonia coordinates, I would first align yourself with the z-axis. Normal rotation moves the viewer not the molecule, so to be sure you are looking down the z-axis you need to use "Align Viewer" to z axis. Nex to align the molecule you just ask to align the tertiary axis (axis of rotation in ammonia) with the z axis. That is, just use "Align Molecules" and align the tertiary axis with the z axis. Your molecule will now have the axis of rotation along Z. For example if you ask to rotate about z by 120 degrees you will have an identical looking system.



HyperChem - Heats of Formation
HyperChem computes energies that give you essentially what you would get out of heats of formation. That is you can calculate the difference in energy (enthalpy) between any two systems. Heats of formation are just a convenient way of tabulating energies (enthalpies). All engines (ab initio included) yield total energies.



HyperChem - DFT using 5 or 6 d-orbitals:
While ab initio calculations can always use 5 or 6 d-orbitals as you choose, the DFT program really wants to use the "conventional" (for quantum chemists) 6 d-orbitals. If you will notice setting the setting at 5 always comes back to 6 thought the GUI (graphical interface). It may seem that you are asking for 5 but the program doesn't like 5 and sets it back to 6 before doing the calculation.

However, if you set this by script (ab initio-d-orbitals 5) and do the calculation, it will crash as the program doesn't currently have a chance to set it to 6 regardless of what the user says. If, as you say, you are using 5 d-orbitals through scripting, the program does indeed crash and currently the only way to fix that is through using 6. However, if you go through the GUI rather than scripts, I cant get it to crash and it only uses 6 d-orbitals no matter what you request.

There needs to be a fix that allows 5 d-orbitals for DFT or a better indication to the user that he/she must use 6 d-orbitals.



HyperChem - Ab Initio Optimization of Excited States:
As for the CI problem, I need to investigate specifically. My first look did indicate that ab initio optimization of excited states was not functioning correctly. This is something rarely used and I don't know if you were trying to optimize an excited state or not. If you are just trying to find the geometry of the ground electronic state just turn on Polak-Ribiere or a decent optimizer and leave conjugate directions alone. In almost every case, CI will give you nothing beyond the simple SCF which because of Brillouin's theorem says that singly-excited states don't mix with the ground state. To use this properly you have to have turned off CI.

If you really want to try and determine the geometry of an excited state, HyperChem is supposed to do it with Conjugate Directions (no gradient information). This is a terrible optimizer but may work when you have no gradient information about an excited state. It may be that this was working in 7.1 and we haven't noticed that it got broken in 7.5. I will check as I say but you don't want to use the procedure you were using if you are just interested in the ground sate.

HyperChem - Newton.exe crashes under Windows XP

There was a problem with the Newton backend on certain versions of HyperChem 7.0/7.1. These caused molecular mechanics calculations on Windows XP to crash. You can download and use an updated version of newton.exe from our ftp site. Please do the following:

1. Download the following file: http://www.hyper.com/downloads/support/newton.exe 

2. Make a backup copy of the newton.exe installed on your drive (usually in the C:\Hyper7\program folder).

3. Replace the installed copy of newton.exe with the one obtained from our site.

4. Try your calculation again.

If you have questions that are not covered here, or need more information please contact us.

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