Re: How to converse Coarse-Grained structure into all-atom structure

From: Axel Kohlmeyer (
Date: Mon May 06 2013 - 05:09:01 CDT

On Mon, May 6, 2013 at 12:02 PM, Fugui <> wrote:
> Dear all,
> 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 cor! responding to the
> coarse-grained structure.
> Could anyone give me some suggestion on that.

how about stripping off the solvent+ions and then convert this
structure back with the existing AA-to-CG mapping?


> Thanks a lot.
> BW
> Fugui

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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