Hi all,
I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it?
Thanks,
Not sure what you are looking for in terms of simple...
https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling is a sample list of options (what you are asking for is in in the "min" column, and many of the other may relate to your longterm workflow ...)
if your on a linux box with a decent sized package manager (anything debian/RHL based including ubuntu, centos, fedora etc, and most of the Arch fam as well) will have a number of options best to look through them and see what works for you>
for if your comfortable with command line look at the Molecular Dynamics family including GROMACs, most of them have friendly online support and have what you'll want and some what you will use later. (they may be a version or 2 behind but for what you're doing that is fine).
If you want a GUI (i.e. must have a mouse) look for things like Avogadro
good luck
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