Perhaps you are looking for "md19.mdcrd"? In your ptraj script you
specify "m19.mdcrd".
-Dan
On Tue, Jun 14, 2011 at 4:14 AM, fatahiya <fatahiyamohdtap.yahoo.com> wrote:
>> ls -lt | grep mdcrd
>
> output:
> -rw-rw-r--. 1 fatahiya fatahiya 217 Jun 14 13:16 md20.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 Jun 3 12:05 md19.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 8831160 Jun 2 11:15 heat7-12.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 189 Jun 2 11:11 heat7-12new_size.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 30 17:55 md18.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 29 16:29 md17.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 28 15:09 md16.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 21677610 May 26 19:04 heat1-6.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 185 May 26 19:00 heat1-6new_size.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 24 16:45 md15.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 23 15:18 md14.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 22 13:53 md13.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 21 12:29 md12.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 20 11:03 md11.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 19 05:17 md10.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 18 03:46 md9.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 17 02:19 md8.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 16 00:45 md7.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 14 23:14 md6.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 13 21:36 md5.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 12 20:04 md4.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 1471855081 May 11 18:39 md3.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 3612930081 May 7 07:19 md2.mdcrd
> -rw-rw-r--. 1 fatahiya fatahiya 3612930081 Apr 28 14:16 md1.mdcrd
>
> thank you for helping me, i'm really new in amber..
>
>
>
>
> ________________________________
> From: Adrian Roitberg <roitberg.qtp.ufl.edu>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Tuesday, 14 June 2011 15:54:29
> Subject: Re: [AMBER] secstruct analysis
>
> ptraj seems to think that there is NO such file in the directory where
> you are running.
>
> Can you do a 'ls -lt | grep mdcrd' command in that directory and send
> the output to me ?
>
> Adrian
>
>
> On 6/14/11 9:52 AM, fatahiya wrote:
>> tq Adrian..
>> after i try again, i put md19.mdcrd in the input file..it shows the same
>>error..
>> is there anything wrong with my ptraj command?
>>
>>
>>
>>
>> ________________________________
>> From: Adrian Roitberg<roitberg.qtp.ufl.edu>
>> To: AMBER Mailing List<amber.ambermd.org>
>> Sent: Tuesday, 14 June 2011 15:16:40
>> Subject: Re: [AMBER] secstruct analysis
>>
>> Well, you WRITE that your input file asks for trajin md20.mdcrd
>> but the ptraj output says otherwise:
>>
>>> PTRAJ: trajin m19.mdcrd
>>> Checking coordinates: m19.mdcrd
>>> Could not process trajectory m19.mdcrd
>>
>> So, the answer is that your input is NOT what you claim it is.
>>
>> I would make sure that the md*.mdcrd files are for sure in that same
>> directory. ptraj is unable to find at least the 19 one.
>>
>> Adrian
>>
>>
>>
>>
>> On 6/14/11 9:12 AM, fatahiya wrote:
>>> i'm trying to do secondary structure analysis
>>> my input file is:
>>>
>>> trajin md20.mdcrd
>>> secstruct out md20.ss time 0.2 :1-20
>>>
>>> the output is:
>>>
>>> \-/
>>> -/- PTRAJ: a utility for processing trajectory files
>>> /-\
>>> \-/ Version: "AMBER 11.0 integrated" (4/2010)
>>> -/- Executable is: "ptraj"
>>> /-\ Running on 1 processor(s)
>>> \-/ Residue labels:
>>>
>>> ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY
>>> GLY PRO SER SER GLY ARG PRO PRO PRO SER
>>> Cl- WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>> ...
>>> WAT WAT WAT WAT WAT WAT WAT
>>>
>>> Setting box to be an exact truncated octahedron, angle is 109.471221
>>>
>>> PTRAJ: Processing input from "STDIN" ...
>>>
>>> PTRAJ: trajin m19.mdcrd
>>> Checking coordinates: m19.mdcrd
>>> Could not process trajectory m19.mdcrd
>>>
>>> PTRAJ: secstruct out md19.ss :1-20 time 0.2
>>> Mask [:1-20] represents 304 atoms
>>> WARNING in ptraj(): No input trajectories specified (trajin), aborting...
>>>
>>> can anybody help me how to do secstruct analysis?
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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>
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Received on Tue Jun 14 2011 - 05:00:09 PDT
