I have performed MD simulation, and have all the results including RMSF, RMSD, PSA etc. Now I want to calculate the Hydrogen bonds made and broken after simulation in the simulated complex on different nano seconds(0, 250,500ns). Can anyone please help me, how I can do that? I have tried Chimera, but it shows there is not any inter HB, although there are several intra HB.
Martin Klvana sorry i didnt get your point, are you asking me to clarify HB in my question or HB in general?
Zumama Khalid, hydrogen bonds are usually defined by distance and angle criteria. What values have you been using?
I am using Distance, and basically I want to check how many new HB are formed after simulation and how many HB broke during simulatio. Martin Klvana
Zumama Khalid, donor-acceptor distance (what is your cutoff value?) is not a sufficient geometrical criterion of hydrogen bond:
https://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/
Assalam O Alaikum
Zumama Khalid
Your HB cut-off criteria 3.0 A. You can open the complex in pymol, which gives great visualizations and measure angle, distance there. But I wanna know that which one software use for MD simulations.
Walikumslam, Waseem Ahmad Ansari I used GROMAX for simulation and I am using PYMOL and UCSF chimera for visualisation.
so you got your requirement??? when you are generating data for RMSD RMSF etc. you can see 2D structure there and analyze HB serial-wise.
Waseem Ahmad Ansari I did the same but chimera is considering simulated complex a single protein not two proteins and only showing intra model HB not intermodal HB.
Look Zumama Khalid exactly what do want ????
Can you please share pic gromacs data file???
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