I used gmx mdmat in gromacs to create contact maps, but I am unable to make sense of the outputs I've got from the same.
Could anyone point me in the right direction?
This is an attempt to simulate the behavior of a membrane protein embedded in a lipid bilyer.
I'm attaching the files.
Any help or comments about the attached files would be appreciated immensely..
Thanks in advance..
Hi Debjyoti,
dm and dmf files will not be the same because one (dm) is an average over the entire simulation, and the other (dmf) has a set of data for each frame in the file (the text file should be much larger). The last file is a ratio (based on what is in the picture).
If you rephrase your question, and indicate what your end goal in, people may be able to better help you.
Cheers,
John
Thanks for the clarification, John..
In response to your comment, I would just say that I want to understand how to read these contact maps..
And gauge what info can be obtained from the same..
Hi Debjyoti Boral
Reading the contact 2D matrix is pretty simple. It just shows which residues are in contact with which others.
Refer to my rough drawing I've attached (contains only 8 residues). Your protein seems to contain about 275 residues.
Just like my drawing, your black/white images have considered residues on both X (1 to 275) and Y (1 to 275) axis. Now, obviously residue 1 is in contact (within a certain distance) with itself. Similarly, residue 2 is in contact with residue 2... and so on. Due to this obvious situation, we see a 45 degree line from lower left to top right corner. Similarly, in my drawing, "x" represents these obvious scenarios.
Apart from these, it is seen from your image that a few residues are in contact with a few other residues, and that is why you see white dots in other regions as well. Similarly, in my drawing, there are a couple of star symbols. These star symbols represent contact between residue 3 and 5 (& vice versa), and 7 and 2 (& vice versa). In your image, if you visualize your residues on the X and Y axis, you'll know which residues are interacting with each other. At least, you'll know which region of your protein is interacting with another.
Every contact is plotted twice. For example, contact dot of 3 and 5, and contact dot of 5 and 3.. represent the same contact but they are plotted twice. One on each side of the 45-degree line. Hence, the image looks symmetrical on both sides of the 45-degree line. This will always be the case.
Hope that was helpful.
- Badges
- Science topic
- Similar topics
- Filing