> /applic/applications/AMBER/64BIT/ESSL//amber10/exe/ptraj 11mer-1-ions-solvate.prmtop << EOF
> trajin mdynamic2.mdcrd 2000 3000
> average 11mer-average.rst restrt
> EOF
I believe the problem is with your script. '<< EOF ' is not a valid
"HereDoc" construct - there should be no space after the '<<'. Remove
that and ensure a newline follows immediately after 'EOF'.
Also, you probably will want to perform an RMS-fit prior to your
'average' command, otherwise you will end up with overall
translational/rotational motion factored into your average structure.
-Dan
On Thu, Apr 24, 2014 at 10:11 PM, 전선희 <jeonsunny.naver.com> wrote:
>
> Hello AMBER users
> I have a problem like this, when I process the average in amber10.
> "WARNING in ptraj(): Could not open input file (trajin), exiting"
> Eventhough I did RMS process by use of ~.prmtop file and ~.mdcrd file, I could not pass the average step with the same file, ~.prmtop file and ~.mdcrd file.
> I attached file..RMS script file, RMS out file, average script file, average out file..
>
> Please tell me what I have to correct....
> Please help ~~~
>
>
>
>
>
> 블로그서명jeonsunny님의 블로그
> 안녕하세요.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Apr 25 2014 - 07:00:02 PDT
