Reply To: flexpep docking problem—–How to do with phosphorylation peptide?

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June 2, 2011 at 10:51 pm #5699
Anonymous

    Sounds like you’re having issues with there not being a p-Ser in the “centroid” residue type set. See http://www.rosettacommons.org/node/2342

    I’m not too familiar with Flexpep docking, but you might be able to avoid the centroid mode phase altogether. You may want to try omitting the “-lowres_preoptimize” flag.