problems with implementing NOE constraints

[Anonymous]

Hi I’m running csRosettaCM with POMONA alignments and I would like to include NOE constraints in my models. Some of my constraints are on the side chains, therefore I cannot implement them in centroid mode, and would like to implement them in the full atom mode. However, it seemed like csRosetta has ignored my cst_fa_file and did not take in the constraints on the side chain. Any suggestion on how to fix this? And if it is possible to run csRosetta in full atom mode directly?

I have the following in my flags file:

-cst_fa_file noe_fa.cst

-cst_file noe.cst

-constraints:cst_fa_weight 10.0

-constraints:cst_weight 10.0

I have the following constraints in my noe_fa.cst file:

#AtomPair: Atom1_Name Atom1_ResNum Atom2_Name Atom2_ResNum Func_Type Func_Def

AtomPair HE1   21    HA2  16   BOUNDED  1.50 4.00 0.30

Thanks in advance for any advice / suggestions.

[Anonymous]

Hi all,

sorry for bringing this up again – but I still haven’t got the NOE constraints to work. I’ve been reading and I think I sorted out some issues but it is not working still.

The problem I had is this error message:

[ERROR] Exception caught by JobDistributor for job S_0808Atom 2HA 13 not found

And it happened when Rosetta is reading through the pdb templates indicated in rosetta_cm.xml (attached)

Rosetta is run with the following command (from POMONA)

$rosettaBin -parser:protocol rosetta_cm.xml @flags -database $rosettaDB -out:file:silent default.out -out:file:scorefile default.sc

And the flags file contains the following (attached)

-cst_fa_file noe.cst

-cst_file noe.cst

-constraints:cst_fa_weight 1.0

-constraints:cst_weight 1.0

My suspision was there were no sidechains in the centroid mode and therefor the atom 2HA is not found, but I simply can’t get Rosetta read in my constraints in the full atom mode. I got full atom models in the end but the constraints were obviously not fulfilled.

I have tried the following constraints:

AtomPair   2HA  16   HE1   21   BOUNDED  1.50 3.00 0.30

AmbiguousNMRDistance 2HA 16 HE1 21 BOUNDED 1.5 3.50 0.3 NOE

I had double checked that the numberings were correct, so the atom was not missing because I have put in the wrong numberings.

I have read that taking out pro_close 1 in stage3_rlx.wts file may help (I don’t understand how…) so I have tried that but it didn’t seem to work either. I have attached the  stage3_rlx.wts file as well.

Again any advice / suggestions are much appreciated.

[Author]

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