On 7/25/16 5:43 AM, flavio seixas wrote:
I generated a model with all hydrogens using allhmodel. Now I want to refine a loop in this model using the script below. However, the hydrogens are being removed in the generated models.
Loop modeling relies on a statistical potential derived from pairwise atom-atom distances extracted from known PDB files. Most PDB files don't contain hydrogens, so this potential includes no terms for interactions with hydrogen. (Even if it did, including hydrogens roughly doubles the number of atoms in your system, which would result in a more rugged energy surface and also roughly quadruple the compute time for little benefit.) If you really want hydrogens in your models, add them in later.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage