Re: Generate missing atoms of a coarse grained structure

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Apr 04 2010 - 07:55:56 CDT

Hi Mert,
the CGTools plugin of vmd provides some functions to help with this --
if you have an original structure, they will translate and rotate the
groups of atoms corresponding to each CG bead to best match the cg
structure, and then create config files to do annealing in the presence
of restraints to relax the structure. You should be sure to resolvate
the structure with atomistic water before running the restraint
simulations. See the "Reverse Previously RBCG Model Back To All-Atom"
heading at http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/. Note
that you need to have files equivalent to those generated during the
forward coarse graining operation in cgtools in order to use this
feature, but if you made your cg model a different way, you can still
make use of them by making .cgc files compatible with cgtools and then
re-coarsegraining your atomistic system just to get the required input
files.

Best,
Peter

Mert Gür wrote:
> Dear all,
> I have predicted a structure of a protein using a coarse grained
> model. i.e. I only have the Carbon Alpha coordinates.
> I also have the pdb file of this protein for a different structure.
>
> What I want to do, is to find the closest realistic structure (with
> all its atoms) to the predicted structure.
> For that purpose I have to first generate the missing atoms of the
> predicted coarse grained structure .
> Then perform an additional short minimization.
>
> I was planning to use TMD for that purpose. Starting with the
> structure provided in the pdb file I will force the carbon alpha atoms
> to go
> to the predicted coordinates and the minimize it.
>
> Do you have better suggestions how to generate the missing atoms of
> the predicted structure .Also any comments/critics on using TMD for
> this purpose will be of big help.
> Best,
> Mert
>

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