Hi all,
I would like to do dynamic cross correlation map analysis with AMBER for the ligand and some selected residues/waters around the ligand it in the pocket. I am wondering how to set arguments in crosscorr. Any help would be appreciated.
Cheers Zahra
I don't know how to do it w/ Amber. However, you can use Normal Mode Wizard in VMD for this purpose. Load your trajectory to VMD. Go to Extensions -> Normal Mode Wizard. Open Prody interface. Select the appropriate atoms to do PCA. Then, fill the tickmark for cc heatmap just before submitting your PCA job.
You will have you cc map as a heatmap (blabla.hm file) and you can visualize it in VMD. Moreover, you can be sure that you selected the correct atoms by visually checking them in VMD.
Dear Zahra,
First you need to extract the complex trajectories/pdb files between the required interval. while doing this, you will get 1 pdb file having different time interval coordinate information, then run CPPTRAJ command like below link:
https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#magicparlabel-31
Or you can use Bio3d software, all you need to convert the Amber trajectories from .nc/.mdcrd to .dcd
good luck
Dear Nivedita Rai
thanks for your suggestion.. I have started with bio3d which looks so handy with given test file but as my trajectory files are so big can not used it interactively with Rstudio interface and have to run it directly with R (trajectories have been converted to .dcd with VMD) . now the issue is it could read the R script but has been stopped at the beginning of that. I could not figure out what is the issue...
Cheers
Zahra
Dear Lei,
so many thanks for your help and sharing the script. I have done in with the bio3d at the end...
Bests
Zahra
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