AMBER Archive (2001)

Subject: Re: problem using xleap and tleap

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Aug 22 2001 - 12:23:27 CDT

        1. I can't load pdb files using xleap and tleap programs. It gives an
        error message like:
        
        ERROR: Syntax error

What command are you giving it (verbatim)? It should be

> x = loadpdb filename

        2. I've ran a simple minimization problem. I've the output file and
        a file with ext. of XYZ. If I want to visualize the file, which
        program should I use. If it is xleap program, what command
        (I used "load" command, but it gave me the same error message).

Assuming the .xyz is a restrt file ('-r restrt' in sander), use
ambpdb to convert to pdb for viewing.

        when I test AMBER with test.all command, it gives
        me an Failer error message when running leap. It says
        "the environment is not set". Even when I set the environment,
        it still gives me the same error message.
        
What shell are you running? What command are you using to set
the environment?

Bill Ross