[gmx-users] Can I put b-factor into xtc file?

[Mark Abraham]

Hi,

I don't know what your intended use case is, but there are various
approaches to get a single PDB frame from a trajectory (e.g. trjconv -dump)
and to combine that with B-factors (e.g. editconf -bf), but frankly the
latter stage is probably easier with your own script, e.g. building on
MDAnalysis (or similar).

Mark

On Thu, Feb 1, 2018 at 10:37 PM ZHANG Cheng <272699575 at qq.com> wrote:

> Thank you Mark for this fascinating tng format. I think I could not modify
> it using C/C++ at this moment.
>
>
> For your "easier approach", do you mean I can convert xtc to pdb frame
> with b-factor assigned, if I provide the b-factor file? How to do this?
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng";<272699575 at qq.com>;
> Date:  Fri, Feb 2, 2018 04:44 AM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  Can I put b-factor into xtc file?
>
>
>
> Dear Gromacs,
> I have residue-based b-factor values for a protein. In the past, they were
> assigned to the b-factor columns of pdb files. It would take a lot of space
> if I extract all the pdb files. As the pdb files come from the xtc file, I
> wonder, if I can modify the xtc file directly?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
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