Rosetta Enzyme design cst block raises error

[Anonymous]

Hi All,

I’m trying to run the Rosetta Enzyme Design protocol and I wrote a cst file for the matching step.

My cst file includes two blocks (I pasted below), they use the exactly same format but when I add the second block the match program starts to report an error.

 

CST::BEGIN

TEMPLATE:: ATOM_MAP: 1 atom_name: O6 P1 O4

TEMPLATE:: ATOM_MAP: 1 residue3: ANA

TEMPLATE:: ATOM_MAP: 2 atom_name: CD2 NE2 CE1

TEMPLATE:: ATOM_MAP: 2 residue3: HIS

CONSTRAINT:: distanceAB: 3.70 0.30 180.00 0 0

CONSTRAINT:: angle_A: 105.6 20.00 100.00 360.00 1

CONSTRAINT:: angle_B: 64.9 20.00 100.00 360.00 1

CONSTRAINT:: torsion_A: -25.4 10.00 50.00 360.00 1

CONSTRAINT:: torsion_B: -119.3 15.00 0.00 360.00 3

CONSTRAINT:: torsion_AB: -172.9 75.00 5.00 360.00 1



ALGORITHM_INFO:: match

  CHI_STRATEGY:: CHI 1 EX_FOUR_HALF_STEP_STDDEVS

  CHI_STRATEGY:: CHI 2 EX_ONE_STDDEV

      IGNORE_UPSTREAM_PROTON_CHI

ALGORITHM_INFO::END

CST::END



CST::BEGIN

TEMPLATE:: ATOM_MAP: 1 atom_name: O1 C2 C1

TEMPLATE:: ATOM_MAP: 1 residue3: ANA

TEMPLATE:: ATOM_MAP: 2 atom_name: CE1 ND1 CG

TEMPLATE:: ATOM_MAP: 2 residue3: ASP

CONSTRAINT:: distanceAB: 3.50 0.30 180.00 0 0

CONSTRAINT:: angle_A: 125.4 20.00 100.00 360.00 2

CONSTRAINT:: angle_B: 146.4 20.00 100.00 360.00 2

CONSTRAINT:: torsion_A: -15.7 10.00 50.00 360.00 2

CONSTRAINT:: torsion_B: 103.3 15.00 0.00 360.00 3

CONSTRAINT:: torsion_AB: 31.1 75.00 5.00 360.00 2



ALGORITHM_INFO:: match

  CHI_STRATEGY:: CHI 1 EX_FOUR_HALF_STEP_STDDEVS

  CHI_STRATEGY:: CHI 2 EX_ONE_STDDEV

      IGNORE_UPSTREAM_PROTON_CHI

ALGORITHM_INFO::END



CST::END

 

The error info is here:

protocols.match.downstream.LigandConformerBuilder: Ligand conformers were split up into 120 match-redundant groups.

protocols.match.Matcher: Begin constraint2

protocols.match.Matcher:  Upstream residue type ASP for geometric constraint #2

protocols.match.Matcher:   ALGORITHM_INFO:: match — chi sampling strategy EX_FOUR_HALF_STEP_STDDEVS for chi # 1

protocols.match.Matcher:   ALGORITHM_INFO:: match — chi sampling strategy EX_ONE_STDDEV for chi # 2

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

terminate called after throwing an instance of ‘std::out_of_range’

  what():  map::at

Aborted (core dumped)

I first checked the naming of each atom and I believe they are there. Then I tried to tune the number of samplings for each line in the second cst block but nothing changed. Could anyone help me understand how to solve these bugs?

 

 

[Anonymous]

Hi All,

I’m sorry for the mistake. The amino acid should be HIS but ASP that’s why the program raises an error. The debug mode is very useful because the release version just sends me some nonsense error while the debug version clearly points out that ASP doesn’t have a CE1 atom. 

[Author]

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