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 |
|( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
| | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ |
| | "This is a Biosheet" (J.G.E.M. Fraaije) |
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