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problem with modelling of protein (140 and 150 residues respectively)

Submitted by krlitros87 on Wed, 2014-10-22 09:39

Category:

Structure prediction

Hello everyone,
i'm having some problems with 2 proteins that have 140 and 150 residues respectively.
By now i have generated only 1000 models (i intend to create 10000 in total), but i'm not having clusters at all :/
I read somewhere that the abinitio method (related to modelling) works on protein with less that 100 residues. Is that correct?
What can i do to overcome this problem?

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https://www.rosettacommons.org/docs/latest/cluster.html

Read more about problem with modelling of protein (140 and 150 residues respectively)
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What are "-nstruct" and "cluster_histogram.txt" for "clustering.py"?

Submitted by lanselibai on Fri, 2014-10-17 06:06

Category:

Structure prediction

Hi friends,
After following

Can I ask something about the usage and how to interpret the results?. It seems that there is not so much information on the website.

# The following is my options
-in:file:fullatom
-out:file:silent /path/to/cluster.out
-run:shuffle
-cluster:radius -1

1. How many decoys per input structure is recommended to specify "-nstruct"?

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Read more about What are "-nstruct" and "cluster_histogram.txt" for "clustering.py"?
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Syntax for the alignment file in "minirosetta comparative modeling"

Submitted by lanselibai on Thu, 2014-10-16 15:29

Category:

Structure prediction

Hi friends,
I am confused about the syntax for the alignment file for homology modeling.

Can I ask
1) If "-cm:aln_format grishin" is specified, in the ".aln" file:

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Read more about Syntax for the alignment file in "minirosetta comparative modeling"
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ab initio modelling - what to do next?

Submitted by krlitros87 on Thu, 2014-10-16 13:05

Category:

Structure prediction

Hi everyone,
Finally i was able to create 10000 models of my 90 residues protein.
By running cluster.linuxgccrelease i got (i guess) 560 clusters:
---
Timing:
Readin:25s
Cluster: 22s
Additional Clustering: 513s
Total: 560
---
But now i don't know what to do.
According to the IsThisModelGood.pdf document, now i have to create a plot RMSD vs score, so as i don't have a crystal structure to use as a reference, i think the best idea will be to use the structure with the lowest energy, right?

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Knowledge check on steric effects

Submitted by pachecoj on Thu, 2014-10-16 09:13

Category:

Structure prediction

Hi,

I am doing packing on PDB ID 1UKU and looking at two solutions my code produces, one having much higher energy than the other. The only difference between them is that the conformation of one of the Tryptophan residues is different, the other 100 or so residues are unchanged.

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Read more about Knowledge check on steric effects
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Calculating binding affinity

Submitted by phanvy on Wed, 2014-10-15 23:35

Category:

Docking

Dear all,
After running Flexpepdock, I want to calculate the binding affinity of peptide (ligand) on protein (its acceptor).
Can someone suggest me the method?

Thank in advance and best regards,
Phan Vy

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Questions on energy oddities

Submitted by pachecoj on Wed, 2014-10-15 13:26

Category:

Structure prediction

Hi,

I am doing side-chain packing on a fixed backbone over a discrete set of configurations. Given a set of (non-rotamer) side-chain configurations I'm using Rosetta to calculate one-body and two-body energies using the standard scoring function. I observe to things that seem strange in the two-body energies:

1) For a pair of residues sometimes the two-body energies are almost all zero except for a couple configurations. This sort of makes sense if the residues are far enough apart, but does it make sense that they are *exactly* zero?

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