[gmx-users] Re: Request
feenstra at few.vu.nl
Thu Mar 8 15:33:15 CET 2007
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).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "This is a Biosheet" (J.G.E.M. Fraaije) |
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