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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> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
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Received on Sat Jun 16 2018 - 08:00:03 PDT
