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RosettaCM Ignoring Ligand

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RosettaCM Ignoring Ligand


I am attempting to predict the structure of a known heme protein after 4 mutations and I have decided to try using RosettaCM. I have included all the proper ligand flags listed in the manual however the output I am recieving has residues that reside where the heme is supposed to be.  The threaded template PDB has the heme added at the end of the file and is on chain X. The program runs fine and produces outputs however I think it is ignoring the Heme. The XML file and flags file are included below. I was wondering if any of you have had this problem before or have any insight into what the problem with my commands are. 

Thank you!


This is my xml file: 

        <ScoreFunction name="stage1" weights="score3" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.5"/>
        <ScoreFunction name="stage2" weights="score4_smooth_cart" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.5"/>
        <ScoreFunction name="fullatom" weights="talaris2013_cart" symmetric="0">
            <Reweight scoretype="atom_pair_constraint" weight="0.5"/>
        <Hybridize name="hybridize" stage1_scorefxn="stage1" stage2_scorefxn="stage2" fa_scorefxn="fullatom" batch="1" stage1_increase_cycles="1.0" stage2_increase_cycles="1.0" add_hetatm="1" hetatm_to_protein_cst_weight="1" hetatm_cst_weight="1"> 
            <Fragments three_mers="frag3.frags" nine_mers="frag9.frags"/>
            <Template pdb="HemThreaded.pdb" cst_file="AUTO" weight="1.000" />
        <Add mover="hybridize"/>



And these are the flags I am using:

-in:file:fasta mutant.fasta
-parser:protocol rosetta_cm.xml
-nstruct 10
-database /home/research/rosetta/main/database/
-default_max_cycles 200
-extra_res_cen HEM.cen.params
-extra_res_fa HEM.fa.params
-extra_improper_file HEM.fa.tors

Post Situation: 
Sun, 2022-12-04 12:05