Re: Generate missing atoms of a coarse grained structure

From: Mert Gür (
Date: Wed Apr 14 2010 - 03:35:13 CDT

Thanks a lot for your help.

On Sun, Apr 4, 2010 at 3:55 PM, Peter Freddolino <> wrote:
> 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 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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