Determining the ring conformation of A-L-Idopyranose during the course of a 10ns MD simulation using BFMP.

If needed, please click here for instructions on downloading and installing the BFMP program.

The program requires three input files: an AMBER format topology file, AMBER format trajectory file and a configuration file.

1. Click here to download BFMP-Tutorial1.tar.gz, the Input AMBER format files and output files for this tutorial.
2. Unpack the archive:

   tar -xzf BFMP-Tutorial1.tar.gz

3. Change to the new directory:

   cd files_BFMPtutorial1/

4. Using vi or any other text editor, open the plain text file (the configuration file) called input.txt containing the following information:

   Atom
   C1
   C2
   C3
   C4
   C5
   O5
   Residue 
   2
   Cut off
   10
   Path
   /pathtoyourtextfile/canonicals.txt

5. Each of the three keywords shown in the file above should be followed in the same order on subsequent lines by the relevant values as described below. For detailed descriptions of these parameters, please read the Documentation available here.
   • Atom: The ring atom names, in order around the ring starting from the first atom. For an aldohexapyranose, the list should begin with the anomeric carbon, with the other ring atoms listed in order moving towards the ring oxygen.
   • Residue: The number of the residue containing the ring whose conformation should be analyzed. In this set of input files, the Iduronic acid  we want to analyze is residue #2.
   • Cut off:  A cut off value of 10° is specified here.  The user can alter this value.  If it is larger, a larger number of structures will be categorized as IUPAC.  If smaller, then fewer will.
   • Path: The path to the text file which is required to run the program. Please make sure to edit this to match the path to your canonicals.txt file which was provided when you downloaded the software.
6. Run the program.

   /path/to/your/detect_shape IdoA.prmtop IdoA.crd input.txt

   Note: According to /usr/bin/time, this command took about 11 s to run on an Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz processor. If you have a similar or faster processor, and it takes much longer than that, something might have gone wrong.  The output file, ring_conformations.txt, should contain 100,002 lines.

7. Check the analysis output
   • If desired, you can compare the output you get to output files we created.  Please note that these files can be compared only if used a 10° cutoff value. If you used a different cut off value they might no longer be comparable. To make the comparison, the “diff” command should do, and, if successful, should give the following output:

     % diff -s ring_conformations.txt ring_conformations_Tutorial-1.txt
     Files ring_conformations.tx and ring_conformations_Tutorial-1.txt are identical

   • The output file has three columns. For example, these might be two lines in the file:

     1      -        5d2(1.543800)           t46(6.649975)
     49     1C4      1d4(1.315064)           5d2(8.650978)         3d6(9.472997)

   • The first line indicates that in the first frame of the simulation there are two best fit four-membered planes below the cut off values specified (10°). However, the combination of these planes and their out-of-plane atoms indicate that this conformation is distorted and cannot be well described using standard IUPAC nomenclature. This is indicated by the –  in the second column.  The second line indicates that in the 49th frame of the simulation, there are three best fit four membered planes below the cut off values specified.  Also, the positions of the out of the plane atoms of these three planes also indicate that this can be described as a 1C4 conformation, and this is listed in the second column.