VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Fri Sep 11 2020 - 06:21:21 CDT

Dear All,

I am studying interactions between a decasaccharide and a trihelical protein (a homotrimeric protein with 70+ amino acids in each chain). The interaction is fairly rapid (within 10 ns) and stable during the 50 ns production run.

I am interested in measuring the distance between each of the 10 sugar residues and the amino acids in the 3 protein chains. I would like to obtain a heat plot where the x-axis shows the time (in ns) and y-axis shows sugar residue number. The colors on the heat plot correspond to the distance between the sugar residue and the protein. I guess 3 plots will need to be generated, one each for chains A, B and C because the sugar residues are binding to the 3 chains. Performing this manually for each of the 10 sugar residues will be extremely time consuming. Is there an easier way (tcl script or VMD plugin?) to determine this and express the distances as a heat plot?

Thank you in advance for your inputs.

Regards,
Raman