AMBER Archive (2004)

Subject: Re: AMBER: imin=5 in sander

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Tue Dec 07 2004 - 14:44:52 CST

Hey,

Try to set ntwx=1 in your input file. The default value is 0 and then
the trajectory file is not opened.

Asim 

-- 
Asim Okur
Stony Brook University
Chemisty Department
Stony Brook, NY 11794-3400
631 - 632 1560

MURAT CETINKAYA wrote:

>Hi Amber users,
>
>I am trying to run sunder with imin=5 parameter for trajectory analysis. But
>sander cannot process my trajectory file. Sander reads rst or inpcrd files but
>gives out this message when I try to run with a mdcrd file:
>
>fmt: read unexpected character
>apparent state: internal I/O
>last format: (i6,e15.7)
>lately reading sequential formatted internal IO
>./min5_EN.q: line 7: 15353 Aborted                 $AMBERHOME/exe/sander -O -i
>min5_EN.in -o min5_EN.out -p 3_20.prmtop 
>-c 3_20.mdcrd -r new.rst -ref 3_20.mdcrd
>
>I realized that there is a number at the beginning of my inpcrd files (something
>like 39150) and that does not exist in a mdcrd file. I suspect that may be a
>reason. 
>
>Is there an intermediate step before analyzing a trajectory file with imin=5?
>
>also my sander input file is:
>minimization_step1
> &cntrl
>  imin   = 5,
>  maxcyc = 1,
>  ntb    = 1,
>  ntr    = 0,
>  cut    = 10
> /
>END
>
>Thanks in advance...
>
>Murat CETINKAYA
>Biomolecular Materials Lab,
>Dept. of Engr. Science and Mechanics,
>The Pennsylvania State University,
>University Park, PA 16802
>office: (814) 863 9967
>web: www.personal.psu.edu/muc176
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