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.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 16 2018 - 07:30:02 PDT
