Re:Re: Generate missing atoms of a coarse grained structure

Date: Sun Apr 04 2010 - 08:25:06 CDT

i always get tens of e-mails which comes from TCB communicators everyday.
i hope you can tell me how to do it.<br><br>在2010-04-04 20:55:56,"Peter Freddolino" <> 写道:
>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
>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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