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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> >>>
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Received on Sat Jun 16 2018 - 07:30:03 PDT
