AMBER Archive (2008)

Subject: Re: AMBER: a question of ptraj

From: WANG,YING (wangying_at_ufl.edu)
Date: Wed Jan 02 2008 - 12:04:24 CST

Hi,
Thanks very much!

Yes, when I delete the frame 0, it works.

Thanks!

Ying

On Mon Dec 31 15:38:21 EST 2007, Chris Moth
<chris.moth_at_vanderbilt.edu> wrote:

> It is possible that $frame is not being expanded as you think
> inside the stdin of ptraj.
>
> You might want to capture and read the stdout of ptraj.
> Perhaps something like this would work:
>
> $ptraj prmtop << EOF | tee ptraj.$frame.output
>
> Or, restruture you loop to create one long shell script with no
> loops, and
> run that instead. If you can create a short script which
> produces the
> required rst file, then you ought to be OK for a longer run which
> repeats
> that code.
>
> The third "offset" parameter to trajin might be useful. If you
> set this
> to 10000 for a 1000 frame coordinate file, that should ensure
> that only
> one frame is processed.
>
> You start with frame=0, but I believe ptraj starts numbering of
> frames
> from 1. That may be part of the problem.
>
>
>> Hi, Dear all,
>> I meet a problem when I use ptraj of amber 9. I only want to
>> extract some frames from the mdcrd file, but the ptraj extract
>> every frame out..
>> Could anybody tell me why? Thanks very much!
>> I paste my script as below:
>>
>> #!/bin/bash
>>
>> ptraj=/apps/amber/9/intel/ptraj
>> for frame in 0 14 21 58 64 77 97 142 153 186 210 241 256 263 332
>> 358 363 379 393 395 396 399 423 432 466 493 497 516 519 535 549
>> 551 575 587 601 645 651 675 716 726 733 746 766 803 813 817 850
>> 867 879 925 931 940 956 964 967 975 976 979 983 984;
>> do
>> echo $frame
>> $ptraj prmtop <<EOF
>> trajin 1b9p_equ.mdcrd $frame $frame
>> trajout frame.rst restart
>> EOF
>>
>> done
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu