[gmx-users] LINCS ERROR WITH LIGAND

[Anton Feenstra]

Raj Badhan wrote:
> Dear Users,
> I am running a PR simulation with a protein + ligand in a water box.
> However, LINCS complains about the usual rotations, but these 
> rotations involve bonds within the LIGAND (ATP) as opposed to the 
> protein.
> Any assitance would be appreciated!

Can you run your ATP in water (without the protein)? Or, if that fails,
can you run it in vacuum? If that works, the topology itself is probably
not the problem. HAve you checked for (bad) contacts between protein and
ATP? Especially, I would think unfavourable charge interactions could be
a potential problem with ATP.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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