[gmx-users] Re: gro to pdb

[Viswanadham Sridhara]

editconf -f  *.gro -o *.pdb
trjconv -f *.trr -s *.tpr -o *.pdb

Make sure * resembles to the appropriate file names you have.
Either one should work.

Cheers,

On 1/10/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Dhananjay wrote:
> > Hello all,
> >
> > When I tried:      trcjonv -f your.gro -o your.pdb
>
> editconf
>
> please read the manual.
>
> >
> > I got following error:      Fatal error: File topol.tpr not found
> >
> > When I tried :      editconf -f *.gro -o *.pdb
> >
> > I got the error as follows:
> >
> > Warning: Number of atoms in prime_b4pr.gro is 0
> > Fatal error: gro file contains more atoms (1075423546) than expected (0)
> >
> > When I tried this :    trjconv -s file.gro -o file.pdb -s topol.tpr
> >
> > the error I got is :       Fatal error: Double command line argument -s
> >
> > Can anybody tell me what is wrong here ?
> >
> >
> >
> > On 1/9/06, Farid Sa'adedin <fsaadedi at staffmail.ed.ac.uk> wrote:
> >
> >>Quoting Dhananjay <dhananjay.c.joshi at gmail.com>:
> >>
> >>
> >>>How to convert .gro file to .pdb file ?
> >>>
> >>
> >>editconf -f *.gro -o *.pdb
> >>
> >>
> >>
> >>Farid Sa'adedin
> >>Membrane Biophysics Laboratory
> >>Department of Veterinary Biomedical Sciences
> >>College of Medicine & Veterinary Medicine
> >>Royal (Dick) School of Veterinary Studies
> >>University of Edinburgh
> >>Summerhall
> >>Edinburgh EH9 1QH
> >>SCOTLAND
> >>
> >>
> >>_______________________________________________
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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