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
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Received on Tue Jun 14 2011 - 01:00:04 PDT
