[gmx-users] Re: Request

[Anton Feenstra]

payal kumari wrote:
> Respected Sir
> I am working on 1T5A,human pyruvate kinase M2.I mutated the protein at 
> position 391 replacing histidine with tyrosine in chin A.After that 
> performed energy minimization using gromacs..Its showed the warning 
> "Water Box Exploded"
> what does it mean and how to remove this..please let me know

It probably means you have (severe) clashes in your 'mutated' protein 
structure. This causes atoms to be pushed away with large forces.

Try to use a (simple) modeling program (e.g., DeepView/SwissPDBviewer) 
to resolve the problem.

By the way, I do not recall that I have seen this error during energy 
minimization, it usually shows up only during MD runs (check your mdp 
settings and mdrun output).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
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|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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