AMBER Archive (2006)

Subject: Re: AMBER: fail to execute addles

From: pang zhao (
Date: Mon May 15 2006 - 09:31:19 CDT

Dear Prof. Carlos,

Great thanks for your kind help.

Now, when I use rcrd, addles works fine.

But after the completion of addles, it generate the, les.crd, and I
want to use the newly generated parameter file to run minimization with
sander.LES using the following command:

nohup sander.LES -O -i -o min.out -p -c les.crd -r min.restrt&

After the execution of above command, In the command line, I
type"top" and fine sander.LES is in run. However, the size of the file
min.out is zero
even when the sander.LES has run long time.
 When I just run 200 steps of sander.LES with a single cpu of 2.5GZ
, after ten minutes, the minimization is still in run . I think it is
abnormal and kill it.

However ,when the sander.LES is killed, the min.out has the following message:

Amber 9 SANDER 2006

| Run on 05/15/2006 at 13:53:49
[-O]verwriting output
File Assignments:
| MDOUT: min.out
|INPCRD: leshpp.crd
|RESTRT: min.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

Here is the input file:

LES minimization

imin = 1,
maxcyc =100,

ncyc = 1000,nsnb=25,
ntr = 0,
ntb = 1,

igb = 0,ntpr=50,


| Flags: LES

getting new box info from bottom of inpcrd

| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info not found in inpcrd

|Largest sphere to fit in unit cell has radius = 0.000

What is the problem?

Best regards
Pang Zhao

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