combine_silent ERROR: unknown atom_name: CYS SG

[Anonymous]

Dear Rosetta experts,

I am trying to combine some silent file representing proteins that have disulfide bonds (combine_silent.linuxgccrelease from rosetta/2015.25.57927).  The silent files were created by running minirosetta for structure determination.  I am running into the following error message:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975

ERROR: unknown atom_name: CYS  SG

Can anyone please tell me how to get around this error?

Thanks,

Holly Freedman

University of Alberta

[Anonymous]

If the first residue in your protein is cysteine, you probably have a centroid/fullatom mismatch, and need a flag (-in:file:fullatom or in:file:centroid ?)  to tell combine_silent you have fullatom silent files, not centroid silent files, or maybe the reverse.

If the first residue in your protein is not cysteine…I don’t know, I’d look at the line of code, but your version is so old it would take a while to find the right revision, so I’d rather wait  to see if the first idea pans out.

[Anonymous]

If the first residue in your protein is cysteine, you probably have a centroid/fullatom mismatch, and need a flag (-in:file:fullatom or in:file:centroid ?)  to tell combine_silent you have fullatom silent files, not centroid silent files, or maybe the reverse.

If the first residue in your protein is not cysteine…I don’t know, I’d look at the line of code, but your version is so old it would take a while to find the right revision, so I’d rather wait  to see if the first idea pans out.

[Anonymous]

If the first residue in your protein is cysteine, you probably have a centroid/fullatom mismatch, and need a flag (-in:file:fullatom or in:file:centroid ?)  to tell combine_silent you have fullatom silent files, not centroid silent files, or maybe the reverse.

If the first residue in your protein is not cysteine…I don’t know, I’d look at the line of code, but your version is so old it would take a while to find the right revision, so I’d rather wait  to see if the first idea pans out.

[Anonymous]

smlewis,

This was extremely helpful – I really appreciate it!

 I’d had -in:file:residue_type_set centroid set and when I removed this, the combine program ran fine.

Holly

[Anonymous]

smlewis,

This was extremely helpful – I really appreciate it!

 I’d had -in:file:residue_type_set centroid set and when I removed this, the combine program ran fine.

Holly

[Anonymous]

smlewis,

This was extremely helpful – I really appreciate it!

 I’d had -in:file:residue_type_set centroid set and when I removed this, the combine program ran fine.

Holly

[Anonymous]

Can I please ask again about the same error from running clustering.py – now I am getting again:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975

ERROR: unknown atom_name: CYS  SG

after running

./clustering.py –silent=../silent.out –rosetta=/global/software/rosetta/rosetta-2015.25.57927/bin/cluster.linuxgccrelease –database=/global/

software/rosetta/rosetta-2015.25.57927/rosetta_database –options=cluster.options cluster_summary.txt cluster_histogram.txt

Is there a similar simple fix for this?

Thanks,

Holly

[Anonymous]

Can I please ask again about the same error from running clustering.py – now I am getting again:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975

ERROR: unknown atom_name: CYS  SG

after running

./clustering.py –silent=../silent.out –rosetta=/global/software/rosetta/rosetta-2015.25.57927/bin/cluster.linuxgccrelease –database=/global/

software/rosetta/rosetta-2015.25.57927/rosetta_database –options=cluster.options cluster_summary.txt cluster_histogram.txt

Is there a similar simple fix for this?

Thanks,

Holly

[Anonymous]

Can I please ask again about the same error from running clustering.py – now I am getting again:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975

ERROR: unknown atom_name: CYS  SG

after running

./clustering.py –silent=../silent.out –rosetta=/global/software/rosetta/rosetta-2015.25.57927/bin/cluster.linuxgccrelease –database=/global/

software/rosetta/rosetta-2015.25.57927/rosetta_database –options=cluster.options cluster_summary.txt cluster_histogram.txt

Is there a similar simple fix for this?

Thanks,

Holly

[Anonymous]

Got it! – I just added -in:file:fullatom to cluster.options

Thanks again,

Holly

[Anonymous]

Got it! – I just added -in:file:fullatom to cluster.options

Thanks again,

Holly

[Anonymous]

Got it! – I just added -in:file:fullatom to cluster.options

Thanks again,

Holly

[Anonymous]

Same error: probably same fix.  I’d guess that “–options=cluster.options” highlights your culprit; look in that file, it’s probably rosetta command line options being passed along from the python clustering.py along to the underling Rosetta call.  (I’ve never used clustering.py but this seems a reasonable guess).

[Anonymous]

Same error: probably same fix.  I’d guess that “–options=cluster.options” highlights your culprit; look in that file, it’s probably rosetta command line options being passed along from the python clustering.py along to the underling Rosetta call.  (I’ve never used clustering.py but this seems a reasonable guess).

[Anonymous]

Same error: probably same fix.  I’d guess that “–options=cluster.options” highlights your culprit; look in that file, it’s probably rosetta command line options being passed along from the python clustering.py along to the underling Rosetta call.  (I’ve never used clustering.py but this seems a reasonable guess).

[Author]

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