Dear Experts in AMBER group,
I am doing a long simulation (using iwrap=1, with water box in rectangle size, 8 A from each side) for a protein complex with 3 protiens (400 residues + 100 residues + 30 residues)
As the center of the complex is the 400 residues protein. As I used iwrap=1, I found the box shifted along the way. I tried several setting in doing ptraj for getting rmsd and rmsf data from the trajectory.
(1) trajin xxx.mdcrd center :1-530 origin # all three protein in one goes image origin center familiar rms first out xxx.rms .CA atomicfluct out xxx.nofactor .CA byres average xxx_average.pdb pdb nobox
I found this is wrong, as I got the averaged structure with all the proteins fragmented. I learnt it from the experts in AMBER archives that I have wrongly center all three proteins to center. So, I change the ptraj file as follows:
(2) trajin xxx.mdcrd center :1-400 origin # only the largest and center part of the protein complex image origin center familiar rms first out xxx.rms .CA atomicfluct out xxx.nofactor .CA byres average xxx_average.pdb pdb nobox
I expecting it could works. However, when I have close look at the average structure, I found the averaged protein pdb file still contain fragmented chains. Most notably, the 30 residues protein (originally located at the top of the 400-residue protein), has now move to the bottom of the 400-residue protein. The rms file has starting values of 2-3 A, but jump to over 50A and back to 3 A along the trajectory. I learnt from achieve that we should the center with small part of the protein. So, I tried once as follows:
(3) trajin xxx.mdcrd center :1-100 origin # small part of the largest and center part of the protein complex image origin center familiar rms first out xxx.rms .CA atomicfluct out xxx.nofactor .CA byres average xxx_average.pdb pdb nobox
However, same results as (2) was obtained. I learnt from achieve that we can do stepwise centering. So, I tried once as follows:
(3) trajin xxx.mdcrd center :1-100 origin # small part of the largest and center part of the protein complex image origin center familiar center :1-400 origin # small part of the largest and center part of the protein complex image origin center familiar rms first out xxx.rms .CA atomicfluct out xxx.nofactor .CA byres average xxx_average.pdb pdb nobox
However, same results as (2) was obtained.
I am out of solution now. Could you mind to share your experiences with me how to get it work. It is a must that we should all the trajectory back to the box without redoing all the long simulations with a much larger water box size?
Best regards,Catherine
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Received on Sun Jul 22 2012 - 20:00:02 PDT
