Atom Repack
Roan Distilo
Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.
Hi,
I am attaching my protein files for you to have a look. I have my native protein as "protein.pdb". I coarse grain it and then perturb my protein backbone a little bit (using PRS, Atilgan et al 2010, Biophysical J). Now I put my side chains back and then I repack it using repacking algorithm from Rosetta. I get my output file as "repacked-protein.pdb". Now all the other side chains are repacked except the loop region from 73-75. After this I also used relax protocol and obtained "relax-protein.pdb" file. But still its not able to minimize properly in the loop region. Do you have any suggestions on how I can solve this.
When you initially said coarse graining, I initially thought of something along the lines of Rosetta's centroid mode, which abstracts the sidechain positions, but keeps the backbone heavy atoms in physiological relevant positions.
Looking at repacked-protein.pdb, it looks like your coarse graining method significantly perturbs the backbone coordinates. Repacking only changes the sidechain coordinates - the input backbone conformation will be preserved if you just do repacking.
By the way, you probably want to omit the backbone constraints in these relax runs, as the input backbone coordinates are not what you want. Alternatively, you could keep the backbone constraints on but remove the "-ramp_constraints false" and/or increase the value to -relax:coord_cst_width to allow more movement. (Value of the last is the size of allowable atom movement in Angstroms.)
Relax is the main protocol for simple all-atom refinement of structures in the Rosetta force-field. Relax does not do extensive refinement and only searches the local conformational space around the starting structure. Relax is thus often used in conjunction with more aggressive sampling protocols like fragment assembly (abinitio) and loop modelling. To evaluate different conformations based on their Rosetta all-atom score one usually has to apply relax.
It can also read centroid models, in which case it will convert the model into a fullatom model and pack the sidechains. Relax does not carry out any extensive refinement and only searches the local conformational space neighbourhood.
Relax returns full-atom relaxed structures. Relax is a general purpose protocol and used in many different applications where fullatom structures are required at the end. In most cases relax is the last step in a larger protocol and the lowest energy structures are of interest to the user.
The fast relax modes work by running many sidechain repack and minimisation cycles ramping up and down the repulsive weight of the forcefield. This sort of "pulses" the structure in successive collapse and expansion phases which "wiggles" the atoms into a low energy state. No explicit moves are done (this was found not to be useful as most moves are rejected and dont help lowering the energy). Not that despite that fact, the structure can change up to 2-3 A from the starting conformation during the minimisation cycles.
The basic principle of the relax protocol is to interlace packing of sidechains with gradient based minimization of torsional degrees of freedom.A typical relax cycle consist of 4 rounds of repacking followed by gradient base minimization in torsion space. The repulsive contribution to the total energy is scaled to 2%, 25%, 55% and 100% in the 1st, 2nd, 3rd and last round, respectively. Relax can be run with a different number of cycles (default is 5) and from all cycles performed the best scoring pose is selected.
FastRelax is a more modern version of the initial fast relax algotihm which is more flexible and allows definition of a specific script of relax events (how exactly the repack and minimisation cycles are interlaced and what paramters they should take). This is defined in a script file. An example script file looks like this:
The above command chain would do 5 repeats of a ramp-profile of 0.02, 0.25, 0.550 and 1.0 of the repulsive weight. At each step a repack is followed by a minimisation with a tolerance of 0.01,0.01,0.01 and 0.00001 respectively. Over all the weight would pulse in this order 0.02, 0.25, 0.550, 1.0, 0.02, 0.25, 0.550, 1.0, 0.02, 0.25, 0.550, 1.0, 0.02, 0.25, 0.550, 1.0 ... The lowest energy structure encountered at the full weight is reported back at the end.
where the mutations of residues i and j to μs and μl must be done in such a way that at least one of the residues is different from the original identities μi and μj. Equation 5 can be substituted into eq 1 to compute the atomistic mutational pairwise frustration Fijmut for Nmut mutational decoys (Nmut = 1000 for this work).
To compute the atomistic configurational frustration, we used decoys that were directly taken from long molecular dynamics trajectories that include folding and unfolding events.22,23 Interactions between any given pair of residues i and j can be observed throughout the protein trajectory. For the purpose of computing decoy energy distributions, we looked specifically at the conformations in the nonfolded states (fraction of native contacts
Relax is the main protocol for simple all-atom refinement of structures in the ROSETTA force-field. Relax does not do extensive refinement and only searches the local conformational space around the starting structure. Relax is thus mainly used in conjunction with more aggressive sampling protocols like fragment assembly (abinitio) and loop modelling. To evaluate different conformations based on their ROSETTA all-atom score one usually has to apply relax. It is further advisable to apply relax only to previously idealized structures. Idealization avoids that score differences arise due to non-ideal geometry (e.g., at the position of former chain-breaks introduced during an aggressive sampling stage and removed by loop closing).
Here are step-by-step instructions for using ChimeraX virtual reality (VR) capabilities to mutate a residue, rotate a bond, and repack the new residue and neighboring residue using interactive molecular dynamics.
Rotate a bond.To rotate a bond of the new side chain to avoid clashes with neighboring residues click on therotate bond icon with the hand-controller.The log area at the top of the panel will say "VR mode bond rotation". Then click on abond and rotate the hand-controller to rotate the atoms on one side of the bond.
Repack residues.To minimize energy of the new residue click on the minimize energy icon with the hand-controller.The log area at the top of the panel will say "VR mode minimize". Then click on anatom of the mutated residue and hold the button down to run molecular dynamics on thatresidue and the contacting residues (within 3 Angstroms).
Tug on atoms.To tug on atoms click on the tug icon with the hand-controller.The log area at the top of the panel will say "VR mode tug". Then click on anyatom and move the hand controller while holding the button down to exert a force onthat atom while running molecular dynamics.
Small proteins. We have chosen a very small protein because currently the molecular dynamics residue repacking we want to demonstrate runs on the entire protein and is too slow on larger proteins. In the future this will be optimized to only run molecular dynamics on a part of the protein. If you wish to try another molecule, it will need hydrogens which can be added with the addh command. Currently only the standard 20 amino acids can be parameterized by our OpenMM molecular dynamics code.
Flickering. Minimizing energy or tugging on atoms causes the graphics to flicker because it is not updated fast enough. To avoid nausea it is best to look in a fixed direction while doing these operations. In the future we plan to run the graphics and molecular dynamics in parallel to avoid this problem.
In my case, the repack had been triggered automatically as part of a git pull. When I got the error, after ruling out a permission issue with a quick sanity check that none of the things that would be launching git processes (IDE, git bash, git GUI) would be running elevated, I went to Process Explorer to find out what process had the file open (Find -> File Handle or DLL), and it found a git.exe that was a parent of the other git.exe process. I'm guessing that there are some locking assumptions in the automatic repack code that aren't appropriate on Windows, where, by default, opening a file puts an exclusive read/write lock on the file at the OS level.
Hello ullassssss,
I would suggest to estimate the target voidfraction and use the insert/stream command in combination with the mass parameter. Please note that you will need some "free space" for the insertion of the elast bit of particles. If possible I would suggest to slightly "overfill" the container and use the delete_atoms command to remove the surplus for making sure that enough material was added.
Cheers,
Alice
WARNING: Particle insertion: Less insertions than requested (/build/buildd/liggghts-3.0.3+repack/src/fix_insert.cpp:646)
ERROR on proc 2: Failed to allocate 869899668 bytes for array neigh:binhead (/build/buildd/liggghts-3.0.3+repack/src/memory.cpp:45)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 1.
Hello,
first of all I'd recommend to generate the particle distribution by definind a couple of different particle templates and combining the to a distribution (see for example packing example in the examples section of LIGGGHTS-PUBLIC, here two particle templates are used in one distribution, more are possible just as well). Then, secondly, make sure that the neighbor bin size is approx. equal to the diameter of the larger sphere (maximum), or, if there are only few of the bigger particles, a bit smaller.
Then, one further remark: you are inserting particles with a volumefaction of 0.625, this is by far too much. I'd suggest a value around 0.2 or maybe 0.25 (watch out for warnings like "WARNING: Particle insertion: Less insertions than requested (/build/buildd/liggghts-3.0.3+repack/src/fix_insert.cpp:646)" in combination with a settling/compression etc.
Cheers,
Alice