From: Fugui (theoreticalchem_at_163.com)
Date: Mon May 06 2013 - 05:02:10 CDT
I finished a coarse grained MD, and i got the trajectory DCD file. I saved the last frame as a .pdb file, but i do not know how to convert it into all-atom structure.
I noticed that VMD can solve the problem. In VMD, Extensions--Modeling--CG builder--Reverse previously RBCG model back to All-atom. However, the all-atom molecule is needed for this transformation.
The problem is that i do not know how to get the all-atom structure. I followed the tutorial of "Residue-based coarse graining using martini force field in NAMD". Firstly, i constructed an all-atom protein-membraned structure, then the all-atom structure is converted into coarse-grained structure, after that, the coarse-grained structure is solvated and ionized. So i do not have the all-atom strucutre corresponding to the coarse-grained structure.
Could anyone give me some suggestion on that.
Thanks a lot.
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