[gmx-users] ATP TOPOLOGIES

[Anton Feenstra]

Daan van Aalten wrote:

> Dear Raj
> 
> If the topology works fine with EM of the compound on its own, then the
> fault lies not with the ATP topology, but the way you incorporate it in
> the overall topology of your enzyme-ligand system. How to do is is very
> clearly defined in John's tutorial. Perhaps you should try as a test a
> different system first. Also you should *NOT* call your molecule "ATP",
> otherwise GMX will get confused as it does have an ATP topology predefined
> in its own forcefield files.

That's not a problem. The ATP in Gromos (and old gromacs) ff is defined as
building block and must be incorporated by pdb2gmx. If you provide your own
itp file defining an ATP molecule, that is fine.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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