[gmx-users] converting .gro trajectory to .pdb

Wed Jan 18 19:59:24 CET 2017

Hi,

Make a PDB file with a single frame the same way you made the gro file with
only heavy atoms. That will have the atom names that PDB output requires.
Then use that PDB file to pass to trjconv -s.

Mark

On Wed, 18 Jan 2017 18:47 Irem Altan <irem.altan at duke.edu> wrote:

> It still asks for a .tpr file, though:
>
> Command line:
>   gmx trjconv -f conf_complete.gro -o file.pdb
>
> Will write pdb: Protein data bank file
>
> -------------------------------------------------------
> Program gmx trjconv, VERSION 5.1.2
> Source code file:
> /Users/irem/Downloads/gromacs-5.1.2/src/gromacs/fileio/gmxfio.c, line: 476
>
> Can not open file:
> topol.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Best,
> Irem
>
> > On Jan 18, 2017, at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 1/18/17 12:32 PM, Irem Altan wrote:
> >> Hi,
> >>
> >> It gives me an error saying
> >>
> >> Fatal error:
> >> Index[1556] 3148 is larger than the number of atoms in the
> >> trajectory file (3145). There is a mismatch in the contents
> >> of your -f, -s and/or -n files.
> >>
> >> I’m guessing this is because I had created the original .gro file by
> just using the protein heavy atoms, but the .tpr file obviously has the
> indices according to the entire system.
> >>
> >
> > You don't need to do anything as complex as what Dawid suggested.  You
> just need to convert the format:
> >
> > gmx trjconv -f file.gro -o file.pdb
> >
> > -Justin
> >
> >> Best,
> >> Irem
> >>
> >> On Jan 18, 2017, at 4:22 PM, Dawid das <addiw7 at googlemail.com<mailto:
> addiw7 at googlemail.com>> wrote:
> >>
> >> Hi,
> >>
> >> I guess you can try
> >> gmx trjconv -f  file.gro -o file.pdb -pbc mol -s file.tpr -center
> >>
> >> 2017-01-18 16:14 GMT+01:00 Irem Altan <irem.altan at duke.edu<mailto:
> irem.altan at duke.edu>>:
> >>
> >> Hi,
> >>
> >> I have a trajectory saved in .gro format. It has multiple
> frames/snapshots
> >> in it. I’m using .gro format because I needed higher precision than
> >> standard .pdb precision, but now I can’t visualize it with VMD. I would
> >> like to convert this to .pdb, and I tried editconf to do this. The
> problem
> >> is, it only converts the first frame. How can I convert the entire
> >> trajectory from .gro to .pdb?
> >>
> >> Best,
> >> Irem
> >> --
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> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
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> >
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