[gmx-users] Re: inconsistency in .pdb files

[h a]

Thank you Mark and Justin, your replies were very helpful . I was converting
output file back into pdb file using "genconf" as I wanted to find out the
structural changes happening(Ex: conformational changes ) after every
operation. Is there any other way to tack progress of my task(Ex: Hydration
) .

Harshith

On Fri, May 30, 2008 at 2:26 AM, h a <y600100 at gmail.com> wrote:

> 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 .
>
> thank you,
>
> Harshith
>
>
>
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