AMBER Archive (2003)

Subject: AMBER: Carnal Input file

From: Frederico.Miranda_at_ibmb.uib.no
Date: Mon Sep 22 2003 - 18:06:55 CDT

Hye, I'm trying to get some data out of a md simulation that I made, using
carnal, but I don't seem to get what I would like to. Could some help me
please? This is my input file for carnal:

____

FILES_IN
  PARM p1 pidimer.parm;
  STREAM s1 pidimer.mdcrd;
FILES_OUT
  COORD c1 pidimer.W120_carbon_ALFA.carnal;
DECLARE
  GROUP carbon (ATOM 1939);
OUTPUT
  COORD c1 s1;
END
_____

What I would like to do is to get the posisiton of a specific atom during a
simulation. My parameter file is pidimer.parm and my coordinates file is
pidimer.mdcrd . I made a PDB file of those two and the atom I want to follow
on the simulation is number 1939 in the pdb (It's the alpha carbon of a
protein's tryptophan). So what I was expecting is a file with a time
parameter, showing the time step of the simulation, in one column and 3
columns with x,y,z positions. But that is not what I got. Could someone help
me? Thank you.

Frederico Miranda

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