[gmx-users] Re: trjconv

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> It is surprising!,
> Because I used -sep option But it made 20 pdb file separately  with 0 byte!
> 

Do you have sufficient disk space?  The only way I can see that you would get 
files of zero bytes are:

1. Not enough space on the disk
2. The frames specified do not exist

-Justin

> On Mon, Nov 8, 2010 at 11:26 AM, mohsen ramezanpour 
> <ramezanpour.mohsen at gmail.com <mailto:ramezanpour.mohsen at gmail.com>> wrote:
> 
>     of course I could generate a pdb file without -b and -e options,but
>     I don't want it.
> 
>     besides I did the same process with xtc file and I resulted in a 0
>     byte file :(
> 
> 
> 
>     On Mon, Nov 8, 2010 at 11:21 AM, mohsen ramezanpour
>     <ramezanpour.mohsen at gmail.com <mailto:ramezanpour.mohsen at gmail.com>>
>     wrote:
> 
>         Dear justin
> 
>         I checked what you said,yes,both of them(trr and xtc files) were
>         completely done as I wanted in my mdp file.
> 
>         what is your points of view?
> 
> 
>         On Sun, Nov 7, 2010 at 9:15 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>             Vitaly Chaban wrote:
> 
>                 Did you try to re-run your trajectory? Does the problem
>                 persist then?
> 
> 
> 
>             Perhaps the faster solution would be to see what gmxcheck
>             says about the trajectory.
> 
>             -Justin
> 
> 
> 
>                     I have a trajectory with 20000 frames.
>                     i want to separate just 1000 last frames of it in
>                     pdb formt and 1000 first
>                     frames too.
>                     I entered this command:
>                     trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800
>                      -e 1000
> 
>                     actually my total time is 1000 ps.
>                     the process was  not  done completely!
>                     when I delete -e option it is done completely but
>                     the the result file is 0
>                     byte,then i can not earn anything.
>                     what is the problem?
> 
>                     thanks in advance for your comments
>                     Mohsen
> 
> 
>             -- 
>             ========================================
> 
>             Justin A. Lemkul
>             Ph.D. Candidate
>             ICTAS Doctoral Scholar
>             MILES-IGERT Trainee
>             Department of Biochemistry
>             Virginia Tech
>             Blacksburg, VA
>             jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>             http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>             ========================================
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================