AMBER Archive (2009)

Subject: RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP

From: Hopkins, Robert (
Date: Wed Apr 01 2009 - 18:10:44 CDT

Drs. Case and Zhang, a little further detailed checking shows that
my AMBERHOME environment variable is correct, but in repeating the
tests of sleap I find that an error occurs whenever I use *any*
environment variable within the program. In fact, the parameter
files are loaded correctly whenever I spell out the path in detail.

Thus, this is not a real problem. Thank you both for your efforts
to help me arrive at a solution.

Bob Hopkins

-----Original Message-----
From: [] On
Behalf Of David A. Case
Sent: Sunday, March 29, 2009 1:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP

On Sun, Mar 29, 2009, Hopkins, Robert wrote:

> Without loading any
> coordinate files, I tried sleap followed by
> source leaprc.ff99bsc0
> to which I got the response:
> Error: can not find file leaprc.ff99bsc0 in all the search path

Works for me. Is your AMBERHOME environment variable set correctly?
Wei: sleap should probably print out the search path when emitting an
error message like the one above.

> Then, I tried:
> source /usr/local/amber10/dat/leap/cmd/leaprc.ff99bsc0
> to which I got the responses:
> Error: can not get bond for the given two atoms: CA H5
> Error: can not find atom C in molecule
> Error: can not find file frcmod.parmbsc0 in all the search path

This is probably the same search path problem as above. And, I don't
see this behavior, so you might make sure you have the latest version of
sleap (AmberTools 1.2), if the AMBERHOME variable is not the problem.


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