I am trying to visulaize h-bonds within my molecule of (.out) gaussian extension. i ticked "display settings" then marked hydrogen bonds, but still no H-bonds are formed. Could you please illustrate how to get the h-bonds network within my molecule.
Hello Muhammad,
H bond usually do not appear because is a large interaction and visualize programs do not draw bond at these distances. Even so, there are few programs that draw the H bonds, for example MacMolPlt. You can try with it.
I hope it helps you,
Joaquim Rius
http://wiki.wxmacmolplt.googlecode.com/git/MacMolPlt_Manual.html
To expand what Joaquim said: there are many definitions of hydrogen bond in terms of minimum/maximum distance and optimum angle between the X-H...X atoms, so many visuazliation programs use different criteria for the formation of hydrogen bond. I'm not familiar with Avogadro, but there are other visualization programs that may help (GaussView, Molden, Molekel, Pymol). Also, in some of them you can define the Hbond criteria yourself, or just draw a dashed line between two selected atoms for visualization purposes, if you're certain that the HBond is present.
First, Thanks so much.
But i want a program which is able to work with (.out) extension and give professional visualization for good publication.
Bartosz,
I just want to draw dashed line between the selected atoms, then i can write the distance, obtained from gaussview, manually.
So I guess Pymol would be a good choice. It probably doesn't read gaussian .out files, but you can easily convert them to .xyz using OpenBabel or something similar. It can definitely draw the dashedline between selected atoms and is able to provide high-quality renderings through the ray (raytrace) command.
Another good choice will be chemcraft.(http://www.chemcraftprog.com/).Trial version is free for 150 days.It can read the gaussian output file as well as other formats.There are some templates(which are customizable) under the display tab.Click on the atoms and press 'ctrl+b' to create a bond between them. Double click the bond and set it to H- bond.You can also show the distance by selecting the two H-bonded atoms and then clicking the show tab.
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