How to visualize interlocking spheres?

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varuniitr
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How to visualize interlocking spheres?

Post by varuniitr » 30 Mar 2016, 14:04

Dear All,

I have completed TPA calculations using IEF-PCM for solvent effects. I want to see the molecular shaped cavity to confirm that whether it is covering my molecule or not. Can I visualize it? If yes, then Please guide me how to do it.

Thanks in Advance !

rob
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Re: How to visualize interlocking spheres?

Post by rob » 30 Mar 2016, 14:07

You can visualize the molecular cavity using the cavity.off file that DALTON produces and the GeomView software: http://www.geomview.org/
Notice that GeomView will only visualize the cavity and not the molecule itself.
Roberto

varuniitr
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Re: How to visualize interlocking spheres?

Post by varuniitr » 30 Mar 2016, 14:12

Thank you very much Rob for such a quick response. I will try and get back here. Thanks again.

varuniitr
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Re: How to visualize interlocking spheres?

Post by varuniitr » 30 Mar 2016, 14:28

I tried it. Yes it is not showing my molecule along with the spheres. Suppose In order to reduce the number of tessarae, I put cavities only on some atoms (say on C-atoms after increment in radii of spheres and no cavity on H-atoms), then How can we check that whether the full molecule is being covered or not.

il_freddy
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Re: How to visualize interlocking spheres?

Post by il_freddy » 30 Mar 2016, 14:59

That is often done. Indeed the radii which are used for CHx fragments are generally with the following radii: 1.8, 1.9, 2.0 angstrom, all multiplied by alpha=1.2. For a CH3 the final radius becomes 2.4. If you limit yourself to these simplifications, you should be on the safe side, when it comes to ensuring that atoms are inside the cavity. On the other hand, there should be a check in the code to see if any atoms are outside the cavity, but I'm not 100% sure about it. I suggest you run a calculation with an obvious cavity mistake (water without a sphere on oxygen) and see if Dalton complains about it or not.

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