Is there any way to preserve metal ions and water molecule after energy minimization?

07 October 2013 1 165 Report

I am trying to refine my protein structure using online servers, however all of them eliminate the metal ions and water molecule which are required in the final structure. Is there any way to prevent this?

Saravanan Parameswaran

As Mr. Girinath mentioned, It is preferable to carry out EM studies offline using MD software. My experience with GROMACS is satisfactory.

As Bioinformatician, We should opt for online servers when there is no alternative. When we carry out the studies, We exactly know what and how we carried out it as well as the customization/analysis in 'in silico' work is simple and most needed.

And Why exactly you want to carry out EM and the use of EM structure for further study should justify the methodology.

Hope my thought shed some light...

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