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Segmentation fault when reading VMD PDB


I receive this output when trying to create a pose from a pdb file I outputted using VMD. Initially, it is giving me an error about "HSD" residues, which I rename to "HIS". Does anyone know what might trigger a segmentation fault at this particular location?

core.pack.pack_missing_sidechains: packing residue number 375 because of missing atom number 8 atom name CD1
core.pack.pack_missing_sidechains: packing residue number 377 because of missing atom number 8 atom name CD1

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does rosetta good at peptide-protein docking?

Generally speak the peptide docking is much more chalenged than protein-protein docking for the peptide backbone is much more flexible than protein. Because of this reason, many peptide docking tools would introduce annealing and solvent model. I am wondering, does Rosetta also good at such kind of work?

If I want to do a peptide docking, may I also use solvent model(such as TIP3 and so on) and annealing during the docking?


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Questions on Applying NOE Constraint

I have finished the fragmentation step using CS-Rosetta (with file aa_t000.xx03xx.v_3 and aa_t000.xx09xx.v_3). Now I want to generate protein structures from them and meanwhile apply NOE distance constraints. I have tried to only build 1 structural model. The resulting pdb structure does not satisfy the NOE constraint. I have the following questions:

(1) what is the appropriate way to check the NOE distance constraints have been applied? In other words, is my expectation (the NOE constraint should be there even though only one model has been generated) right?

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why docking results are different?

I use the low resolution protein docking these days. In one case,I use full atoms during protocol to generate 10000 poses and top 200 best score poses were clustered by cluster protocol. In another case, I just generate the 10000 pose with protein backbone and also cluster the top 200 best score poses. I found that the results between these two cases are different.

I am wondering which one should I use for the final protein docking solution?

Thank you very much

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cluster error

I've generated one PDB file containing several strucrues of the same protein MD trjactory by VMD. I try to use the cluster protocol to cluster my structure, but it is always says: the PDB format can not recognize by Rosetta. I also split the one file into different indivisual structural files, but the error is still there.Could you please give me some advices for this issue?
Thank you very much.

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Bug in ?

It seems that there is a bug in When I use this mover in my protocol, my programme exit with en error from BackrubMover::add_segment() function (input pose is null). So I read the code and found that the author may forget to set the input pose. I added two line codes after line 135 in Now it works.

line 134: protocols::moves::BackrubMover backrubmover;
line 135: backrubmover.branchopt().read_database();

/////////////////////my codes//////////////////////////////////

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general question about protein docking

I am wondering what's the general steps for Rosetta protein docking. I found there are two methods people usually use for protein docking by rosetta:

Method one:
low resolution docking(only backbone)-->cluster-->high resolution docking

Method two:
low resolution docking(only backbone)-->cluster--> relax (add sidechain with full atoms)-->high resolution docking

I am wondering which one is much more reliable?

Thank you very much

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Loop modeling with ligand in the receptor

I have docked ligand in a receptor and now I want to perform a loop modeling. I tried using these flags:
-in::file::extra_res_fa aral.params
-loops::extra_res_fa aral.params
... but rosetta returns; ERROR: Option matching -in:extra_res_fa not found in command line top-level
Without these flags Rosetta returns:
ERROR: unrecognized aa ARE
(ARE is my ligand).

So, how do I get loopmodel to recognize my ligand?


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