This is a fairly simple question but I can't find the answer anywhere else online. If have a group of molecules which are not bonded, how do I move the entire group without explicitly adding temporary bonds? In my case I am working with several thousand water molecules, so adding explicit bonds or moving one by one would be extremely tedious. Is there any way to select them all and move them as one molecule?
I think that the best way is operating directly on the Z-matrix of your system, so that by modifying the distance between two atoms belonging to different fragments, all the atoms of the fragments are moved together.
In this context, GaussView cannot help you. I would use Molden, which allows to modify by hand the Z-matrix and seeing directly the effect on your system.
Molden is a free software, working on many OSs and can be obtained from here: http://cheminf.cmbi.ru.nl/molden/
I think that the best way is operating directly on the Z-matrix of your system, so that by modifying the distance between two atoms belonging to different fragments, all the atoms of the fragments are moved together.
In this context, GaussView cannot help you. I would use Molden, which allows to modify by hand the Z-matrix and seeing directly the effect on your system.
Molden is a free software, working on many OSs and can be obtained from here: http://cheminf.cmbi.ru.nl/molden/
I agree with the recommendation from Prof. Arca. Using the Z-matrix editor in Molden would be the best tool to do this with. This is especially true if you are making systematic translations to your cluster. It may seem tedious at first but once you get the hang of it, you'll stick to Molden for most of your needs.
I would like to add the movement of n clusters is possible via GUI in the Linux version of GaussView. There you can select multiple clusters and using a combination of the movement hotkeys (shift, alt, etc.) you can move any number of fragments at once. To the best of my knowledge, this only works in the Linux version of GaussView since the Linux (and Windows?) version lacks the complete set of movement hotkeys.
In case you do not have access to the Linux version of GaussView and would like to refrain from using a Z-matrix editor, several other programs suited for material and crystal growth may be useful. For instance, OLEX2 is a great free program that allows near full manipulation of multiple fragments in large clusters.
I hope this helps. Good luck!
Suppose if you have .mol2 file or .pdf file containing groups of molecules say ligand and water molecules, you can delete the water molecules using chimera visualization tool.
Please follow the steps
1. Open the .mol2 or pdf file in chimera
2. Click the select menu and select which one is to be unchanged For example: Ligand
3. In the next step, select invert selection
4. It will select all the remaining molecules in the system except ligand.
5. Now click delete and save as new file.
In this way, you can have only ligand in your mol2 or pdf file.
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