[gmx-users] question about pdb file

Mike M nmr.mike.nmr at gmail.com
Wed Jun 13 11:41:01 CEST 2012

> Dear Gromacs users
> I have encountered in pdb data bank with Human interferon crystal
> structure:
> http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF
>  It is mentioned that it contains 24 structures. I opened the file and
> saw there are 24 models there.
>  Now if I want to do some simulations on this protein, how should I know
> which model to select
> You get 24 model because that structure was not determined by X-Ray
> diffraction, but by NMR. With the structure calculation from the X-Ray data
> you obtain a single converged structure, whereas by NMR you get an ensemble
> of all conformations that have been detected in your sample solution.

   You can use any of the 24 structures, since you are going to perform a
MD run. During your running, the other 23 conformations are likely to be

>   and when doing pdb2gmx, I should delete the other models?
> Yup, just use one model.
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