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Error when trying to use xml script to design PDB

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Error when trying to use xml script to design PDB

I am trying to mutate and relax the 7ah0 pdb using the following xml script:



<ScoreFunction name="sfxn" weights="ref2015"/>



<Index name="res1" resnums="388A"/>

<Index name="res2" resnums="389A"/>

<Index name="res3" resnums="390A"/>

<Index name="res4" resnums="391A"/>

<Index name="res5" resnums="392A"/>

<Index name="res6" resnums="393A"/>

<Index name="res7" resnums="552B"/>

<Index name="res8" resnums="553B"/>

<Index name="res9" resnums="554B"/>

<Index name="res10" resnums="555B"/>

<Index name="res11" resnums="556B"/>

<Index name="res12" resnums="557B"/>

<Index name="res13" resnums="1304C"/>

<Index name="res14" resnums="1305C"/>

<Index name="res15" resnums="1306C"/>

<Index name="res16" resnums="1307C"/>

<Index name="res17" resnums="1308C"/>

<Index name="res18" resnums="1309C"/>

<Index name="res19" resnums="1290B"/>

<Index name="res20" resnums="1291B"/>

<Index name="res21" resnums="1292B"/>

<Index name="res22" resnums="1293B"/>

<Index name="res23" resnums="1294B"/>

<Index name="res24" resnums="1295B"/>

<Not name="seqfixed">

<Or selectors="res1,res2,res3,res4,res5,res6,res7,res8,res9,res10,res11,res12,res13,res14,res15,res16,res17,res18,res19,res20,res21,res22,res23,res24"/>






<OperateOnResidueSubset name="repack" selector="seqfixed">



<DesignRestrictions name="Establishedmutations">

<Action residue_selector="res1" aas="C"/>

<Action residue_selector="res2" aas="C"/>

<Action residue_selector="res3" aas="C"/>

<Action residue_selector="res4" aas="C"/>

<Action residue_selector="res5" aas="C"/>

<Action residue_selector="res6" aas="C"/>

<Action residue_selector="res7" aas="C"/>

<Action residue_selector="res8" aas="C"/>

<Action residue_selector="res9" aas="C"/>

<Action residue_selector="res10" aas="C"/>

<Action residue_selector="res11" aas="C"/>

<Action residue_selector="res12" aas="C"/>

<Action residue_selector="res13" aas="C"/>

<Action residue_selector="res14" aas="C"/>

<Action residue_selector="res15" aas="C"/>

<Action residue_selector="res16" aas="C"/>

<Action residue_selector="res17" aas="C"/>

<Action residue_selector="res18" aas="C"/>

<Action residue_selector="res19" aas="C"/>

<Action residue_selector="res20" aas="C"/>

<Action residue_selector="res21" aas="C"/>

<Action residue_selector="res22" aas="C"/>

<Action residue_selector="res23" aas="C"/>

<Action residue_selector="res24" aas="C"/>


<InitializeFromCommandline name="EPS"/>

<SetIGType name="linmemig" lin_mem_ig="true"/>









<FastDesign name="design"








<Add mover="design"/>


<OUTPUT scorefxn="sfxn"/>


And i receive the follwing error:


ERROR: Error in core::pose::selection::get_resnum_list(): A residue index could not be parsed.

ERROR:: Exit from: src/core/pose/ line: 179

is it possible for this to be an error with the pdb? I am asuming that it might be a issue with rosetta parameters.

Post Situation: 
Fri, 2023-02-24 13:29

What it probably means is that you have a residue index specification which isn't present in your protein. Double check your inputs to make sure that all the residues you think are present are present. Also check the tracer output to see if there's any warning messages about ignoring/discarding residues due to issues. (Check the occupancy column for the residues too -- by default Rosetta ignores atoms with zero occupancy. You can either correct that in the PDB, or add `-ignore_zero_occupancy false` to the command line to change that behavior.)


By the way, the Index selector should be able to take multiple residue specifications as a comma separated list (instead of ORing them together separately). And most things which can take a residue selector (like the Action of the DesignRestrictions operation) can deal with residue selectors which yield multiple residues, basically applying the same behavior to each. This may allow you to clean up/simplify your script a bit.

Fri, 2023-02-24 13:58