AMBER Archive (2000)

Subject: carnal

From: Prem Raj Joseph (prbj_at_hotmail.com)
Date: Thu Jul 13 2000 - 12:04:30 CDT

Respected Sir,

I tried using the below carnal( given in the carnal manual) script
to pick the water around the DNA molecule. I used the awk command
ie ( awk '$2 < 3.0 {print $1}' file.min > temp ) to pick those
within 3.0 A dist from the solute. From the resulting output I find
that out of the total of 4522 water oxygen 4357 are WITHin 3.0 A DISTANCE
FROM
THE SOLUTE. HOW COULD THIS BE POSSIBLE. what could be the mistake in the
input or the trajectory file.
the file all.imaged.Z contains 1000 frames (1ns run)
when I used the watershell command in ptraj to get a count of number of
waters in each of the coordinate frames , there were about 450 waters within
3.4 A and about 800 within 5 A on an average.

Thanks in advance

Prem Raj

+++++++++++++++++++++++++++++++++++
# ======Coordinate Selection: waters: use of INH2O with DISTRIBUTION MIN

# use of INH2O with DISTRIBUTION MIN - 1st pass
FILES_IN
  PARM p1 bdna25n.top;
  STREAM s1 all.imaged.Z;
FILES_OUT
  DISTRIBUTION d1 file MIN;
# ^this is the key: creates "file.min"
DECLARE
  GROUP g1 (SOLUTE);
  GROUP g2 (ATOM TYPE OW);
# ^^ have to use OW

OUTPUT
  DISTRIBUTION d1 0.0 10.0 10 DIST g1 g2;
# ^^^^^^^^^^^ you'll also get the
# net curve; RAW ok
# ^^^^ this is the 2nd key
# ^^^^ order is solute then
# solvent
END

+++++++++++++++++++++++++++++++++++++++++++

Below is the put put file

++++++++++++++++++++++++++++++++++++++++++++++++++++++++
                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin
># ======Coordinate Selection: waters: use of INH2O with DISTRIBUTION
>MIN
> # use of INH2O with DISTRIBUTION MIN - 1st pass
>FILES_IN
> PARM p1 bdna25n.top;
Reading parm file (bdna25n.top)
parm: opening bdna25n.top
bdna25n.top title:
2',5' BDNA
> STREAM s1 all.imaged.Z;
Using default parm (bdna25n.top) for STREAM s1
(box will be read from stream)
stream: opening all.imaged.Z
>FILES_OUT
> DISTRIBUTION d1 file MIN;
># ^this is the key: creates "file.min"
>DECLARE
> GROUP g1 (SOLUTE);
first water: res = 55, atom = 907 (O )
** Group g1: 906 atoms
> GROUP g2 (ATOM TYPE OW);
** Group g2: 4522 atoms
># ^^ have to use OW
>
># GROUP g1 (RES NAME DGB DGM DGL DCB DCM DCL);
># GROUP g2 (RES NAME CIO);
># GROUP g2 (RES NAME WAT);
>OUTPUT
> DISTRIBUTION d1 0.0 10.0 10 DIST g1 g2;
** group 1 is g1
** group 2 is g2
># ^^^^^^^^^^^ you'll also get the
># net curve; RAW ok
># ^^^^ this is the 2nd key
># ^^^^ order is solute then
># solvent
>END
(EOF reached on all.imaged.Z)
STREAM s1: no more files/crds (iteration 1000)
SUMMARY

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

#############################################
Prem Raj B.J.
Dept. of Crystallography and Biophysics
University of Madras
Guindy Campus
Chennai 600 025
email : prbj_at_hotmail.com , premraj_at_cyberspace.org
phone : 8253224 (residence) , 2351367 (Dept)
#############################################

________________________________________________________________________
Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com