Hi,
Removing the go from the file solved the problem - perfect! Why I do not
quite understand.....
Why does VMD keep the bond between the two hydrogens in the water
molecules?
On Mon, Aug 16, 2010 at 2:18 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> How many atoms are in your system? I can't reproduce this problem with
> a 1000 frame trajectory of 49115 atoms.
>
> It seems from your ptraj output that you are using an earlier version
> of ptraj (<AT 1.4). Is this the case? If so, upgrading to ptraj from
> AT 1.4 may work.
>
> Here's something else to try that is a long shot but has worked for me
> with previous versions of ptraj. I notice that you are passing your
> input file in as STDIN. Does the segfault occur if you remove the 'go'
> from the input file and pass it to ptraj as an argument instead? E.g.:
>
> modified ptraj.in:
> trajin md_0_5.mdcrd
> trajout md_0_5_re_image.mdcrd
> center :1-1000
> image familiar
>
> execute with:
> ptraj PRMTOP ptraj.in
>
> -Dan
>
> On Mon, Aug 16, 2010 at 4:01 AM, Jorgen Simonsen <jorgen589.gmail.com>
> wrote:
> > Hi
> >
> > I am want to re-image my simulation but I get the segmentation fault
> from
> > the simulation. My complex is rather big so I wonder if this is the
> problem
> > or if the issue is my simulation data?
> > My input file is
> >
> > trajin md_0_5.mdcrd
> > trajout md_0_5_re_image.mdcrd
> > center :1-1000
> > image familiar
> > go
> >
> > where the 1-1000 are protein atoms when I execute the script
> >
> >
> > ptraj protein_solv.prmtop < re_image_traj.ptraj
> >
> > it runs through
> >
> > PTRAJ: go
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 125 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File (md_0_5.mdcrd) is an AMBER trajectory (with box info) with 125 sets
> >
> > OUTPUT COORDINATE FILE
> > File (md_0_5_re_image.mdcrd) is an AMBER trajectory (with box info)
> >
> > ACTIONS
> > 1> IMAGE familiar by molecule to box center using the first atom, atom
> > selection * (All atoms are selected)
> > IMAGE familiar, center is at box center
> >
> >
> > Processing AMBER trajectory file md_0_5.mdcrd
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .........................Segmentation fault
> >
> > How to fix this - more memory or ?
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Aug 16 2010 - 06:30:07 PDT
