AMBER Archive (2003)

Subject: Re: AMBER: Carnal Input file

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 22 2003 - 18:23:27 CDT

> 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

If you want the coordinates of that atom in the coordinate
file, you need to put the group id in the final COORD statement.

> ... 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.

You could post-process the mdcrd file with e.g. an awk script
(or a perl script, or visual basic, etc) to put it in the form
you want. Possibly adding a group with one atom to an OUTPUT
TABLE statement would cause that atom's coordinates to appear
in the table. However there is no way for carnal to know what
time steps you are using and how often you print to mdcrd, so
unless carnal's input language were extended to give a way to
specify this, there is no way it will appear in carnal output.

Hence you must postprocess the carnal output (no matter how you
get it) to add the times in the 1st column.

Bill Ross

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