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 - 08:00:02 PDT
