Analyze chair/boat conformation from MD simulation trajectory. Part1 Principle.

I was asked to do this, since one of my project contains seven-membered ring. Although the criterions for chair/boat conformation for six-membered, seven-membered ring are very clear. But it is hard for me to program to achieve that.

I thought for a while and found a stupid way to do this.

First of all, I want to clarify that the result I want is the number of boat/chair conformation at each frame.

My solution is to CLASSIFY all the conformations into groups according RMSD.

The detailed process is below. (Assuming I have 100 conformations at each frame, and 200 frames).

  1. For each residue ID, calculate the RMSD using the conformation of each frame as reference. You should get 200 output files for each residue ID. You should have 100 * 200 = 20000 output files.
  2. For each residue ID, from frame 1 to frame 200, compare RMSD with the rest 199 frames. Find the frame number when RMSD < 0.2 of this residue. The reference frame number and related frame number will be recorded. During the comparison, if the frame has been found to be the related frame in the previous comparison, they would not be used as reference frame. You should have a file record reference frame number and related frame number for each residue ID. So, there will be 100 output files.
  3. According to the reference frame number of each residue ID, extract their conformations and repeat Step 1 and Step 2. You will find some new reference number for all residues in all frames. In this step, the output file should record the reference “residue ID and frame number” with related “residue ID and frame number”.
  4. According the reference “residue ID and frame number” to exact the conformation and check them with VMD, manually determine boat or chair conformations. Record “boat” / “chair” with reference “residue ID and frame number”.
  5. So you can use reference “residue ID and frame number” combined with output files in Step 2 and Step 3 to know the detailed conformation at each frame.

I will post the script in Part 2. This method might have slight “overlapped” results, since some conformations might have RMSD < 0.2 with several reference. Only one reference will be chosen. This will not affect the result, because boat are still boat, and chair are still chair, although the atom arrangement might have some difference.


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