IMP-users February 2021

imp-users@salilab.org

6 participants
3 discussions

RRT Sample with DNA
by John Stiller 01 Mar '21

01 Mar '21

Hello All, Does the rrt sample module support DNA? It seems to not be dividing the molecule into rigid bodies like it does for proteins. I assume I just need to tell it that it's DNA and not protein, but I can't figure out how... Thank you in advance. Best, John *My attempt: * rrt_sample Test_DNA.pdb Linker.txt *Result:* Starting reading pdb file Test_DNA.pdb WARNING Could not determine CHARMM atom type for atom "O2'" in residue #2 "DG" WARNING Could not determine CHARMM atom type for atom "O2'" in residue #3 "DT" WARNING Could not determine CHARMM atom type for atom "O2'" in residue #5 "DC" 2 residues 0 bonds were read from file Linker.txt # atoms 83 # bonds 87 # angles 131 # dihedrals 172 4 bonds were added # atoms 83 # bonds 91 # angles 131 # dihedrals 172 begin ForceFieldParameters0::get_force_field_atom_type: WARNING Atom #9 "O2'" (O) does not have a known CHARMM type end ForceFieldParameters0::get_force_field_atom_type *Rb 0 created with 83 atoms* *1 rigid bodies were created * rb order 0 --> 0 parent 0 0 joints were constructed ProteinKinematics done Init RRT Start RRT run *ERROR: No degrees of freedom to sample!* DNA Molecule Example: ATOM 1 P DG 2 120.209 118.900 144.134 1.00210.77 A P ATOM 2 C5' DG 2 117.681 119.487 143.764 1.00210.77 A C ... Linker.txt: 3 4

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Specification of symmetry groups file for imp_sampcon --ambiguity option
by Jan Kosinski 25 Feb '21

25 Feb '21

Hi guys, What is the specification of the symmetry groups file for imp_sampcon --ambiguity option? Best, Jan

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PMI crosslinks and state ambiguity
by Andrea Graziadei 23 Feb '21

23 Feb '21

Hello, I am building a system using topolgyReader in PMI in imp-2.13. I have built a 2-state system by bm = IMP.pmi.macros.BuildSystem(m, force_create_gmm_files=False) bm.add_state(topology) bm.add_state(topology2) I then add crosslinks to the system with IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint How does the system handle the state ambiguity? If a crosslink is satisfied at a particular frame only in state1, it should count overall as satisfied (given crosslinks are measured on in solution ensembles), also when for example analysing %ge violations with imp-sampcon or similar modules... >From what I understand, It looks to me like this is handled correctly in the sampling, but imp-sampcon and pmi_analysis are not yet equipped to deal with this (slicing on %ge over length does not report crosslinks as satisfied if they are under maximum distance in one of the states only). Is this correct? Many thanks, Andrea

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IMP-users February 2021