Dear Matias I have already tried putting "," as you mentioned but I am
still getting the same error as I explained in my last mail.
On Sat 16 Jun, 2018, 11:48 PM Matias Machado, <mmachado.pasteur.edu.uy>
wrote:
> Dear Atul,
>
> I don't think using "<<! ... !" should be a problem in bash... As Rodrigo
> stated before, there is a name issue in curves... I don't know why but
> curves refers the AMBER trajectory format as *.trj and expects that
> extension, which is confusing. A simple file renaming should solve the
> problem...
>
> ln -s wat1_image.mdcrd wat1_image.trj
>
> Maybe someone can mail Richard Lavery to ask for a change in the input
> settings of curves...
>
> Notice, the *.mdcrd file is a *.crd plane text (ASCII) format with a
> different name extension, I guess there are historical reasons for that...
> So you don't need to re-process the trajectory provided you set ntxo=1 in
> the input file, otherwise you are misnaming a NetCDF file (the default) and
> you do have to use command "trajout file.crd" in cpptraj
>
> I guess the error *Program received signal SIGSEGV: Segmentation fault -
> invalid memory reference.* isn't a file format issue but a typo in the "
> cur.in". If you look carefully the command line, you are missing a ","
> between ",ions=.t. lis=prop," to separate "ions" and "lis" input options...
>
> Best,
>
> Matías
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://www.pasteur.uy]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Bill Ross" <ross.cgl.ucsf.edu>
> Para: amber.ambermd.org
> Enviados: Sábado, 16 de Junio 2018 11:56:23
> Asunto: Re: [AMBER] Trajectory format
>
> Thanks Atul,
>
> I would try using something other than '!' for your 'stop word', since i
> is a special character. If that doesn't help, and there is a way to put
> the input in a file and pass that to the program, it should help debug.
>
> Bill
>
> On 6/16/18 7:36 AM, ATUL KUMAR wrote:
> > Thank you bill.
> > Here is the cur.in:
> >
> > rm prop*.*
> > /4TB_DRIVE/Software/curves+/Cur+ <<!
> > &inp file=wat1_image.trj, ftop=DNA_Water.prmtop, ions=.t. lis=prop,
> > lib=/4TB_DRIVE/Software/curves+/standard, &end
> > 2 1 -1 0 0
> > 1:23
> > 46:24
> > !
> >
> > *Atul Kuamr jaiswal*
> > Research Scholar
> > School of Computational and Integrative Sciences
> > Centre for Computational Biology and Bioinformatics (CCBB)
> > JNU,New Delhi
> > India.
> >
> > On Sat, Jun 16, 2018 at 8:01 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> Please paste your cur.in file, so we can see line 8.
> >>
> >> Bill
> >>
> >>
> >> On 6/16/18 7:23 AM, ATUL KUMAR wrote:
> >>> Dear Mr. Rodrigo, Thanks for your reply. I tried as you suggested in
> the
> >>> last mail but still, I am getting the following error:
> >>>
> >>> *Program received signal SIGSEGV: Segmentation fault - invalid memory
> >>> reference.*
> >>>
> >>> *Backtrace for this error:*
> >>> *#0 0x7FEF8F56AB57*
> >>> *#1 0x7FEF8F56B15E*
> >>> *#2 0x7FEF8EA8054F*
> >>> *#3 0x7FEF8EADA668*
> >>> *#4 0x7FEF8F629728*
> >>> *#5 0x7FEF8F62DC5B*
> >>> *#6 0x409DE3 in intop_*
> >>> *./cur.in <http://cur.in>: line 8: 27478 Segmentation fault*
> >>>
> >>>
> >>>
> >>> *Atul Kuamr jaiswal*
> >>> Research Scholar
> >>> School of Computational and Integrative Sciences
> >>> Centre for Computational Biology and Bioinformatics (CCBB)
> >>> JNU,New Delhi
> >>> India.
> >>>
> >>> On Sat, Jun 16, 2018 at 7:36 PM, Rodrigo Galindo <
> >> rodrigogalindo.gmail.com>
> >>> wrote:
> >>>
> >>>> Curves+ only accepts plain text trajectory files. From CPPTRAJ export
> >> your
> >>>> file as cdr ( trajout traj.crd). Then you can change the extension to
> >> trj.
> >>>> This file will be accepted by Curves.
> >>>>
> >>>> Rodrigo
> >>>>
> >>>>> On Jun 16, 2018, at 12:09 AM, ATUL KUMAR <atul44_sit.jnu.ac.in>
> wrote:
> >>>>>
> >>>>> Thanks for the reply. Actually, I already tried the script you
> suggest
> >> in
> >>>>> last mail.
> >>>>>
> >>>>> parm file.prmtop
> >>>>> trajin file.mdcrd
> >>>>> autoimage
> >>>>> trajout file.trj
> >>>>>
> >>>>> But the .trj file I get by doing so is same as .mdcrd file it's just
> >> like
> >>>>> renaming the trajectory file. And when I use this .trj file for
> curves+
> >>>> and
> >>>>> canion tool for base pair parameter and and ion distribution
> >> calculation,
> >>>>> the tool does not take this .trj file as input.
> >>>>>
> >>>>> So the above method to get .trj trajectory file did not help.
> >>>>> Once again thank you for your reply.
> >>>>>
> >>>>>
> >>>>> *Atul Kuamr jaiswal*
> >>>>> Research Scholar
> >>>>> School of Computational and Integrative Sciences
> >>>>> Centre for Computational Biology and Bioinformatics (CCBB)
> >>>>> JNU,New Delhi
> >>>>> India.
> >>>>>
> >>>>> On Fri, Jun 15, 2018 at 6:46 PM, emanuele falbo <
> >>>> falbo.emanuele.gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>> Dear,
> >>>>>>
> >>>>>> Create a file ptraj.in with following options :
> >>>>>>
> >>>>>> trajin file.mdcrd # the name of the trajectory
> >>>>>> image center
> >>>>>> trajout ptraj.out # the name of the output
> >>>>>>
> >>>>>> then from the terminal run :
> >>>>>>
> >>>>>> $AMBERHOME/bin/cpptraj file.prmtop ptraj.in
> >>>>>>
> >>>>>> you will be getting your proccesed output, of you which you can
> watch
> >>>> the
> >>>>>> trajectory by means of visualization programs such as VMD ...
> >>>>>>
> >>>>>>
> >>>>>> Best Regards,
> >>>>>> Emanuele
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> 2018-06-15 14:02 GMT+01:00 ATUL KUMAR <atul44_sit.jnu.ac.in>:
> >>>>>>
> >>>>>>> Dear amber users,
> >>>>>>> I want to convert my amber trajectory (md1.mdcrd) to .trj
> trajectory
> >>>>>>> format. Can anyone help me with that?
> >>>>>>> Your help is highly appreciated.
> >>>>>>>
> >>>>>>> *Atul Kuamr jaiswal*
> >>>>>>> Research Scholar
> >>>>>>> School of Computational and Integrative Sciences
> >>>>>>> Centre for Computational Biology and Bioinformatics (CCBB)
> >>>>>>> JNU,New Delhi
> >>>>>>> India.
> >>>>>>> _______________________________________________
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Received on Sat Jun 16 2018 - 11:30:02 PDT
