distances definition in course-grained (centroid mode) steps

[Anonymous]

I would like to define a potential between the CB atoms of a certain pair of residues in both centroid and full-atom refinement steps during Abinitio protocol. While in full-atom representation there is no ambiguity, I was wondering if the position of the CB is represented correctly in the centroid mode or this position would be the center of mass of the “super-atom” that represent the side chain, for example. If is not the first case scenario, would it be possible to calculate was it the difference between the “actual” position of CB-like atom in the centroid mode and the position it will be present in the full-atom representation? (I imagine it is a constant…).

ps. I know it would be an alternative to define in terms of CA atoms, but defining in terms of CB atoms implies an aditional accuracy to the potential.

[Anonymous]

~/ROSETTA/Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa hosts the centroid parameters files.  You will see that CB atoms are present in these parameters.  I spot checked a few and the CB position was similar to where it is in the fullatom params.  I expect CB is essentially correct; its sterics are important for ramachandran, after all.

[Anonymous]

~/ROSETTA/Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa hosts the centroid parameters files.  You will see that CB atoms are present in these parameters.  I spot checked a few and the CB position was similar to where it is in the fullatom params.  I expect CB is essentially correct; its sterics are important for ramachandran, after all.

[Anonymous]

~/ROSETTA/Rosetta/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa hosts the centroid parameters files.  You will see that CB atoms are present in these parameters.  I spot checked a few and the CB position was similar to where it is in the fullatom params.  I expect CB is essentially correct; its sterics are important for ramachandran, after all.

[Anonymous]

ooh, someone did write it.  It’s in-code at source/src/core/chemical/residue_io.cc in a big comment midway though the file.

 

[Anonymous]

ooh, someone did write it.  It’s in-code at source/src/core/chemical/residue_io.cc in a big comment midway though the file.

 

[Anonymous]

ooh, someone did write it.  It’s in-code at source/src/core/chemical/residue_io.cc in a big comment midway though the file.

 

[Anonymous]

Pasting from the developer chat:

“Yeah, the docs in that file are the best description of the params file. There is also some high slightly higher level discussion in the Drew et al. NCBB paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067051)”

[Anonymous]

Pasting from the developer chat:

“Yeah, the docs in that file are the best description of the params file. There is also some high slightly higher level discussion in the Drew et al. NCBB paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067051)”

[Anonymous]

Pasting from the developer chat:

“Yeah, the docs in that file are the best description of the params file. There is also some high slightly higher level discussion in the Drew et al. NCBB paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067051)”

[Anonymous]

That is good news!

Is there a place where I can access what is the meaning of each of those parameters? I mean, a description of the file… Right now, I am trying to infer them.

[Anonymous]

That is good news!

Is there a place where I can access what is the meaning of each of those parameters? I mean, a description of the file… Right now, I am trying to infer them.

[Anonymous]

That is good news!

Is there a place where I can access what is the meaning of each of those parameters? I mean, a description of the file… Right now, I am trying to infer them.

[Anonymous]

The params file format is older than 2007, which is a roundabout way of saying no.

• The ATOM lines define which atoms exist (and what their chemical types are in 3 different formats, and I think partial charge)
• UPPER_CONNECT and LOWER_CONNECT define where the connections to the next residue go (the peptide bond)
• BOND lines define connectivity
• ICOOR_INTERNAL lines define the geometry of connections.  The numeric parameters are a bond torsion, angle, and length defined for the connection of the atoms in the last 4 columns.  How the (possibly improper) dihedral maps to those is almost clear; I don’ know how angle and bond length maps.  

I’m ignoring the other fields but can attempt to answer a specific question.

 

[Anonymous]

The params file format is older than 2007, which is a roundabout way of saying no.

• The ATOM lines define which atoms exist (and what their chemical types are in 3 different formats, and I think partial charge)
• UPPER_CONNECT and LOWER_CONNECT define where the connections to the next residue go (the peptide bond)
• BOND lines define connectivity
• ICOOR_INTERNAL lines define the geometry of connections.  The numeric parameters are a bond torsion, angle, and length defined for the connection of the atoms in the last 4 columns.  How the (possibly improper) dihedral maps to those is almost clear; I don’ know how angle and bond length maps.  

I’m ignoring the other fields but can attempt to answer a specific question.

 

[Anonymous]

The params file format is older than 2007, which is a roundabout way of saying no.

• The ATOM lines define which atoms exist (and what their chemical types are in 3 different formats, and I think partial charge)
• UPPER_CONNECT and LOWER_CONNECT define where the connections to the next residue go (the peptide bond)
• BOND lines define connectivity
• ICOOR_INTERNAL lines define the geometry of connections.  The numeric parameters are a bond torsion, angle, and length defined for the connection of the atoms in the last 4 columns.  How the (possibly improper) dihedral maps to those is almost clear; I don’ know how angle and bond length maps.  

I’m ignoring the other fields but can attempt to answer a specific question.

 

[Anonymous]

Thank you smlewis!

 

I will take a look. It was of a great help!

[Anonymous]

Thank you smlewis!

 

I will take a look. It was of a great help!

[Anonymous]

Thank you smlewis!

 

I will take a look. It was of a great help!

[Author]

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