Amber-MD
Regarding Minor/Major groove width analysis with base-pair number
Hi developers. I hope you are fine. I'm a fourth-year PhD student from IIT Delhi. I've started working on ligand-binding to DNA using in GROMACS software. I've installed the cpptraj and tried to calculate the minor/major groove width with the number of base-pairs from my .XTC file. It'll be nice if you tell me the protocol.
!/bin/bash RAY="dna_nvt.gro" # starting coords TOP="../dna_amber.top" # Amber prmtop or GROMACS .top TRAJ="x_dna_major.xtc" # trajectory
cpptraj $TOP <<EOF trajin $RAY trajin $TRAJ
autoimage nastruct NA naout NA groovecalc 3dna run '''''''' I'm using this script. Is it fine?
Sorry for the delay. I've been traveling the past few days and have no laptop (I'm writing this on my phone).
That looks OK. I don't think you need to including your starting .gro file unless you want it for a specific reason (it's not bad to include, just might be unnecessary). The groove width is in one of the three files produced by nastruct. Check the manual for full details. Are you encountering any problems?
Thanks @drroe for your message. I did not face any issues while running the code. I got BPstep.NA file after running the code. In this file, I have major and minor groove widths with BP1 (base-pair 1) and BP2 (base-pair 2). In cpptraj's documentation, I found that cpptraj uses El Hassan & Calladine’s Mid-Strand Correction method. In this method, for each k = 3 . . . N − 3, compute d⊥ for the two minor chords and one major chord. Average over the ensemble to obtain MinGW(k) and MajGW(k). I want to plot the minor/major groove width vs base-pair index. But how can I assign the proper base-pair index?
Hi, sorry this fell off my radar. The situation at where I work has been difficult the past few months so my response time is way down.
I'm having some trouble understanding your desired outcome. What do you mean by proper base pair index? Maybe an example would help me understand.
Sir, I think cpptraj does not treat the assignment of groove width to base-pair steps in a proper way. I'm looking for the following analysis
Hello! If I understand your plot correctly, you have a platinum based compound interacting with the DNA duplex, that means that the structure is going to change and the groove masurements are going to be different from the control (black line). The analysis is doing the right thing on detecting the different structure caused by the Pt compounds.
I think cpptraj does not treat the assignment of groove width to base-pair steps in a proper way.
Do you have an instance where CPPTRAJ is not assigning the number you expect?