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

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 1 17:27:12 CEST 2008

Quoting h a <y600100 at gmail.com>:

> 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
> ) .

If you mean simply setting up your system, the no conformational changes should
be happening.  The only thing that will cause structural changes should be an
actual simulation.  If you want to verify your structures at different stages
of preparation, there is no need to continually convert between .pdb and .gro;
a visualization program like VMD reads both.  Otherwise, if you need a .pdb
file, use editconf, not genconf, as Mark already pointed out regarding the
genconf documentation.


> 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
> >
> >
> >


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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