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 - 08:00:04 PDT
