AMBER Archive (2004)

Subject: AMBER: imin=5 in sander

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Tue Dec 07 2004 - 13:07:34 CST

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