[gmx-users] Re: gmx-users Digest, Vol 54, Issue 1

Ragnarok sdf fabracht1 at gmail.com
Wed Oct 1 08:40:34 CEST 2008

Well, I didn't shuffle or sort my system prior to running. I am running in
parallel, would that be part of the problem?
I have tryed -fit or -pbc but the structure comes out bad the same way. The
exact problem is that I have two structures. Each comes from individual
dynamics job. Now I need to align them so that I can run another job to
study the interaction between them. I have tryed using spdbv and sybyl for
that. spdbv completely mess up my structure. Sybyl tells me that there is
more than one model in my file, and how many of them I would like to load.
Chimera works, but I cannot seem to be able to join both structures and
manipulate them in order to obtain the starting positions for the structures
that I want.
Thank you in advance
Fabrício Bracht

> Hi Fabricio,
> You can also sue the option -dump 10000 to extract a frame. But it's
> not related to your error.
> Have you done any fitting and pbc related stuff or did you
> shuffle/sort your system prior to running?
> Cheers,
> Tsjerk
> On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <fabracht1 at gmail.com> wrote:
> > Hello,
> > I have ran a simulation with gromac but can't seem to be able to extract
> a
> > single structure of a determined frame from my .trr file. I wish to
> obtain a
> > pdb file good for reading in CHIMERA, for example.
> > I tryed the following command:
> > trjconv -f sim.trr -s trjtop.tpr -o pdbiwant.pdb -b 10000 -e 10000.
> > Some programs, spdbv, for example, completely mess up my structure,
> making
> > bonds where it shouldn't etc etc. CHIMERA simply cannot find any
> coordinates
> > in the file. But the .pdb generated from trjconv looks ok. I mean , there
> > are coordinates and all.
> > Any suggestions?
> > Thank you in advance
> > Fabrício Bracht
> >
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