Hello.

Try check these with FMA (http://xray.bmc.uu.se/~jochen/fma.html) or ProDy (http://www.csb.pitt.edu/prody/).

Best Regards.

Hi,

ProDy is a helpful tool that works great for me. In combination with VMD NMWiz plugin for visual analysis it can give you a nice visualization of your results. FMA seems to be interesting too but is only ported to GROMACS thus if you are not gromacs user you have somehow to transform your trajectories.

Proteins are studied with molecular mechanic or MM. The general minimization methods are steepest descent and conjugate gradients. Latter methods use first derivatives of geometries with respect to position variables, while you need to second derivatives of geometries with respect to position variables in frequency calculation. if you need to determine normal modes of special part of protein, after obtaining its equilibrium geometry and minimization with steepest descent and conjugate gradients, cut off the special part. Now, hydrogen atom are added to the cut positions of special part . please select latter hydrogen and model build them. I think, web lab viewer do that itself, every time you add a hydrogen atom. then frequency of the part is calculated in Gaussian software without any optimization.