I start to work in computational chemistry and I use as imput file of my algorithm a pdb standard format, I need all atoms for my calculation (also hydrogens), but frequently the examples I found are without hydrogens. I have used the command h_add and it works: it add hydrogens, but the names are diffrent from the standard pdb format. I explain in pdb format the name of hydrogen depends on the position that it has in the aminoacyd structure ( for example 1HB is the first hydrogen linked to C-beta , but if I add hydrogens with h_add I obtain a sequence of hydrogens labeled as H01,H02,...
Is it possible to obtain labels in standard pdb format?
Thank you very much,
        Bernardetta Addis


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