[gmx-users] How to use the dummy atom?

[Anton Feenstra]

PeiQuan Chen wrote:
[...]
>        CH3
>        |
>     Ph-C-OH.       (R.S)
>        |
>        Dummy atom
> 
> I want to know how to use Dummy atom to represent the molecule.
>    Can anyboby give me some hints to how the creat the latter molecular top files? Because I haven't 
> any experience on use the dummy atoms, I wish you can give me a example top file for it. 

I don't see that you need dummy atoms. If you use united atoms, there is no
hydrogen atom attached to the central Carbon; it will be a 'CH1' atom type,
e.g. a Carbon-Hydrogen united atom. You do noeed to add an improper
dihedral to keep the right tetrahedral arrangement of the Ph, CH3 and OH
groups around the central C. (You'll probably want 2 topologies, one R and
one S).


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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