Dr Case,
I figured out the problem I posted before in my first email. The answer is I didn't define the x[] right, which should be 3*the number of atoms. Then I used the revised input to do testing with a small DNA molecule. It works (see the last email I sent you). However, when I used the same input to test a larger system, there is a new error:
"allocation failure in vector: nh = -4617656057229413269"
I attached all input and output for your reference. I guess there is some memory allocation issue. If any way to solve it, let me know.
Thanks
Xuelin
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of David A. Case
Sent: Wednesday, February 20, 2008 5:19 PM
To: amber.scripps.edu
Subject: Re: AMBER: NAB to calcuate entropy. .
On Wed, Feb 20, 2008, Wang, Xuelin wrote:
>
> Here are the output, input pdb file and nab input file. I used a small
> DNA molecule to do testing. It works without using nsnb=99999. Is it
> right?
Now I am confused...when does it fail? Did the files you sent show a failure?
Can you reproducibly change only nsnb and go from "good" to "bad" results?
Please only send files that show a problem.
...dac
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Received on Sun Feb 24 2008 - 06:07:15 PST
