[gmx-users] inconsistency in .pdb files

[Justin A. Lemkul]

Quoting h a <y600100 at gmail.com>:

> Dear users,
>
> I am a beginner with gromacs. I converted a sample pdb file to gromacs file
> using "pdb2gmx" and then converted it back to pdb file using "genconf" but I
> found that positions of atoms was changed and so was their thermal factor. I
> did not understand why there was change in position of the atoms. when I
> observed both of them using pymol I found  inconsistency in type of atoms
> and bond locations.
>
> can you please explain why this happened .

What were the *exact* commands that you issued?

It's not surprising that the B-values and such were eliminated following
pdb2gmx; as far as I know they're not used for anything.  The output .gro file
contains only coordinates at that point.

-Justin

>
> thank you,
>
> Harshith
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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