To Add All Or Only Polar Hydrogens
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9.5 years ago

Hello everybody,

Got a simple doubt. Do I need to add all hydrogens or only polar hydrogens to my protein before doing energy minimization in SPDBViewer/DeepView?

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Try What-IF webserver to add hydrogens. h_add in pymol will also add hydrogens. Using gromacs to add hydrogens can mess up everything. Also try looking at openbabel.

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Why does GROMACS "mess everything up"? Most programs add hydrogens following geometric criteria and then refine them somehow. The only thing I can think of is the naming, but then, GROMACS is surely the best bet since it supports a large array of forcefields and you are likely to find the one you are using.

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I am saying from >4 years of experience in using Gromacs. You can just take complex structure without any hydrogen, add hydrogens by gromacs, minimize the energy and see what happens..

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Well, I never heard of GROMACS mistreating a protein just because of hydrogens. If adding hydrogens and minimizing blows up your structure, your structure is wrong, not the hydrogen adding routine.. Pymol will add hydrogens using only geometrical criteria, therefore not even doing a minimization. WHATIF does perform some minimization, so it's as good as GROMACS in that regard, but has the added bonus of using a knowledge-based method to optimize the hydrogen bonding network. It also has the 'bad' side of adding hydrogens with creepy names that usually follow no standards so importing them in any other software will cause it either to crash or to ignore those hydrogens.

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I always use WHATIF for adding hydrogens. Adding hydrogen in Pymol in only for visualization purpose.

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7.4 years ago
João Rodrigues ★ 2.5k

It all depends on the forcefield you are using. United-atom forcefields like GROMOS will only need polar hydrogens since all others are considered in the parameters for the heavy atoms they are attached to. Others, like AMBER or CHARMM, are usually all-atom and will add all. I never used SPDBViewer/DeepView, and I'm usually against using molecular visualization tools like SwissPDBViewer and PyMOL for purposes other than visualization. My suggestion is to try and use GROMACS, which is free, fairly simple to install/compile and use, and is suited exactly for this kind of analysis.

Edit: noticed after writing the answer that this was an 'updated' question by the Biostar Community user... anyway, the answer stands. Someone might find it useful.

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