Re: [AMBER] Unit 5 Error on OPEN:

From: mathew k varghese <>
Date: Tue, 17 Mar 2009 11:22:08 +0000


Do you have all the input files(, .prmtop, .inpcrd or .rst)  in the same directory where you are running the program? Try making a new directory, copy all the iput files to that directory and check the permissions of all the files. (use ls -l command).Which is your machine type, os, your status? do you have root permissions? If so try run the program as root to check it is due to permission problems.



Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



--- On Tue, 17/3/09, Nancy <> wrote:

From: Nancy <>
Subject: [AMBER] Unit 5 Error on OPEN:
Date: Tuesday, 17 March, 2009, 2:41 PM

Dear all,

    I am sorry to send this letter again , i am using amber10 in linux .When  i use Sander to make minimization of solvent(explicit solvent),

 $AMBERHOME/exe/sander -O -i -o nan.out -p nan.prmtop -c nan.inpcrd -r nan.rst -ref nan.inpcrd
The input and output files are in the attachment .
It showed that Unit 5 Error on OPEN I have tried many times and i am sure the directory is right, then i tried example B1 of amber tutorials about DNA ,just  made the same mistake ,i do not konw where is wrong, can any body  help me ?
Thanks in advance!

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Received on Wed Mar 18 2009 - 01:15:39 PDT
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