Dear Nandine and Pablo,
It's really quite tricky to use ptraj, I need more study.
I generated the binpos file because it's half sized compared to .crd one,
and it makes a huge difference when you're downloading it from the server
(2x less coffee on my blood....)
it works fine now
thnx
On Thu, Jun 9, 2011 at 11:04 AM, Nadine Utz <nadine.mmb.pcb.ub.es> wrote:
> I had many problems with imaging as well. Make sure you use the wet
> trajectory, if you want to have as well the trajectory without waters,
> remove them after the image/center commands.
>
> Good luck, Nadine
>
> On 06/09/2011 03:53 PM, "Pablo I. D. Dans Puiggròs" wrote:
> > I don't know why you want to convert the .crd file, but you can put all
> > the command in only one ptraj file (i.e. converting, center, re-image,
> > rmsd -in that order-).
> >
> > El 09/06/2011 15:47, Bruno Rodrigues escribió:
> >> Hi Pablo,
> >>
> >> I am converting the .crd file to binpos file and from that I run the
> rmsd.
> >>
> >> Should I put this command when I convert to binpos or when I run the
> rmsd?
> >>
> >> On Thu, Jun 9, 2011 at 10:34 AM, "Pablo I. D. Dans Puiggròs"<
> >> pdans.mmb.pcb.ub.es> wrote:
> >>
> >>> Hi Bruno,
> >>> Try this in the same ptraj run. First center the first strand, then
> both:
> >>>
> >>> center :1-10 mass origin
> >>> image origin center
> >>>
> >>> center :1-20 mass origin
> >>> image origin center familiar
> >>>
> >>> Good luck,
> >>> P.
> >>>
> >>> El 09/06/2011 15:28, Bruno Rodrigues escribió:
> >>>
> >>>> Dear all,
> >>>>
> >>>> I'm running a normal MD simulation of a 10 base pairs DNA in a water
> box
> >>>> with 8A from the last atom to the border in Amber 11.
> >>>>
> >>>> However, under the course of the simulation, part of the DNA escaped
> from
> >>>> the box and sometimes the double strand splits and one of the parts
> goes
> >>>> to
> >>>> the next periodic cell. It is making the RMSD to jump at ery high
> values.
> >>>>
> >>>> I've tried all the re-imaging commands on ptraj, like *image
> familiar*. I
> >>>> put below some of the commands I tried in *ptraj*:
> >>>>
> >>>> *1 -
> >>>> *
> >>>> center :1-20 mass origin
> >>>> image familiar
> >>>> *
> >>>> 2 - this is the command I'm using for running the rmsd of the backbone
> >>>> *
> >>>> trajin 1D20_wat_salt10prod.binpos
> >>>> image familiar
> >>>> rms first mass out 1D20_wat_salt10prod2.rms @P,O3',O5',C3',C4',C5'
> time
> >>>> 0.2
> >>>>
> >>>> thank you in advance
> >>>> *
> >>>> *--
> >>>>
> >>> Pablo D. Dans Puiggròs, PhD
> >>> Molecular Modelling& Bioinformatics Group
> >>> Institute for Research in Biomedicine
> >>> Barcelona Science Park - Spain
> >>> pdans.mmb.pcb.ub.es
> >>> pablo.dans.irbbarcelona.org
> >>> &
> >>> Biomolecular Simulations Group
> >>> Institute Pasteur of Montevideo - Uruguay
> >>> pdans.pasteur.edu.uy
> >>>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Jun 09 2011 - 08:00:02 PDT
