More examples and tutorials are available in other pages. We also have a trouble -shooting page, where there are some tips on how to use antechamber. Amber 10 Tutorial antechamber: strange molecules get parameter files antechamber & leap • antechamber is predominantly a file converter. However, it can be. This section of the tutorial introduces the AMBER programs/tools necessary to set -up the input files .. Let’s try using antechamber on our file.
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In this antechamberr we are only going to apply the HSMD method to the ligand in this system, so we start by removing from the file the header, the antwchamber part, the crystallographic waters and also the hydrogens in the SB3 residue we’ll put them back later.
The resulting file is SB3-noH. To generate the files we need for the MD in Amber, we use the programs Antechamber and Leap, antechambber are included in the package AmberTools, freely available at http: Below are the commands we need to perform in Antechamber: In this way we generated the 3 files that Tleap will need next, SB3.
So now let’s run tleap: We have just created the following 3 files: The last two files are the ones needed for the molecular dynamics simulation. Now we are going to add water around the ligand. This could have been done in the previous step, but if we want to do tutirial now, maybe because we want to try with different amounts of water, we can do it in tutoial way, again using Tleap: We’ve just prepared a These are the files we will use for the simulations: We also created SB3-wat Now we are going to perform a minimization and equilibration, in order to relax the system.
Then, we’ll do a longer simulation checking that the ligand remains in the same microstate from which we are going to extract some frames.
This will allow us to calculate the entropy of the structures in each frame, and its average. This number will represent the entropy of the microstate. Below, we detail the 3 steps of the initial simulation minimization, equilibration and productionwith the input and output files, and the commands needed in Amber to perform the simulations:.
One should check carefully that simulations above went fine, that the system is well equilibrated, and that the ligand remained, during the production run, in the same microstate otherwise, we will be measuring the entropy of more than one microstate. Now, we would usually extract about 80 frames from the previous simulation production runand proceed to the reconstruction of each of them.
In this way, we would obtain the entropy corresponding to each frame, and from there the average. By using a large number of frames, we are tutorrial to reduce the error standard deviation of the average entropy. Since this implies working with a big number of files, and the trajectories from each reconstruction are very big files, here we are going to proceed with only one frame.
In order to extract frames from the previous simulation, we can use the Ptraj utility, that comes in AmberTools. This will extract one structure every 12, between frame 1 and of the initial trajectory.
Now that we have the parameter and coordinate files, we are ready to start the reconstruction of this frame. Essentially, what the script does is:. Production – 60 ps – Reconstructing SB3 with water. We see that the above files are identical, except for the bellymask line, where we tell Amber which atoms are allowed to move during the MD.
2014 AMBER tutorial with HIV Protease
But that, in the present system, means waters, but waters are represented in the next part of bellymask. In the first step, all the atoms to be reconstructed can move: In the second step, all the previous atoms can move, but one: In the last step, only one of them can move.
So we see that, according to the theory, we are doing runs where initially the whole chain SB3 moves, but then, one by one, their atoms are getting fixed.
Note that this script needs you to specify some things, like the path to amber, the name of the prmtop file without the extension and the succession of atoms by atom number that we need to reconstruct in the list antcehamber atoms in the script, we don’t include neither hydrogens nor one atom in the rings; their contribution is expected to be very small, and it will save us some computing time.
Also verify that the file names are correct. So we will need to add a correction to this at the end. The next version of the reconstruction programs here available will also include the motion of these 3 atoms. Also note that this script tuforial execute the reconstruction in a serial way, i.
It is easy to adapt the script to a parallel version in which all the atoms are reconstructed simultaneously. When this script is executed correctly, we obtain a lot of files inputs, output, restarts and trajectories: With this, we are ready to proceed to the analysis of the results.
We need now to analyze the trajectories of each reconstructed atom. This will allow us to extract the entropy for each atom and thus, for the frame. This script has two parts. The program knows which atoms this are, because abtechamber also need to supply an angle file, which contains the list of angles to be treated at each step of the reconstruction analysis.
This list has to specify, in each line, the number of four atoms, where the four are needed to measure the dihedral angle of the last one the one we are reconstructingand where the last three are needed to measure the bond angle of the last one. The angle sntechamber for our case is this.
In that matrix, the columns represent a different angle, and the rows represent a different step in the production run. The output is the entropy of the frame we are studying frame in the present case. If we start we several frames, then the output will be the average entropy of all the frames. Looking inside the script, we see that some parameters need to be fixed, e.
Notice that the generation of the angles matrix takes a relatively long time, while the calculation of S is fast. Below, we present the results for the average entropy of 80 frames framethe one we have been using so far, and the other 79 frames we didn’t use for the sake of simplicityas a function of the bin size and the number of trajectory points used for the analysis. The first column in the table represents the integer, n, by which the maximum dispersion of the angles in the trajectories is divided, in order to define the bin size.
Below, in Figure 1, we have a plot of the entropy as a function of the inverse of the bin size, where we see a nice convergence as the size is decreased we should mention that this convergence is obtained only because in the processing we are increasing the size of the bin if the count on that bin is less than And in Figure 2, we also see a plot of the entropy as a function of the number of data points. Here, we can see that we are approaching convergence, but are not quite there yet.
In general, it is very difficult antechsmber achieve convergence in the number of data points. But we are generally interested in differences of entropies e. But it’s easy to calculate this probability, if we think that we are constructing this three points in space, and we use the correct assumption that these atoms don’t have any preference with respect to their location, other than respecting the correct relations between them e.