Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools

From: FyD <>
Date: Sun, 13 Oct 2013 09:45:40 +0200

Dear Sajeewa Pemasinghe,

> This is the first time I am using RED tools. I am following the tutorial.
> I ran the on my pdb and got the corresponding p2n file.

to compare Ante_R.E.D. 2.0 vs Ante_R.E.D. 1.x

> I then ran the optimization in gaussian using the gaussian input file
> generated by I renamed the p2n file as Mol_red1.p2n and
> the gaussian log file as Mol_red1.log and ran the

this is correct; this means you use
$OPT_Calc = "Off" & $MEPCHR_Calc = "On"

you could also use $OPT_Calc = "On" & $MEPCHR_Calc = "On" and provide
only the P2n file(s) as input(s)


> I get the message
> 'uname' is not recognized as an internal or external command,
> operable program or batch file.

there is something wrong... Which operating system do you use?

> * Operating system *

You can find in the source code:

print "\n\t\tERROR: DO NOT RUN THIS SCRIPT AS ROOT !\n\n"; $check=0;
if($XRED eq "ON"){ print "\t\tPress Enter to exit.\n\n"; <STDIN>; } exit(0);

> I cannot figure out what has gone wrong. Perl is in my path and the RED
> tools folder is in the path. Could anyone please help me out? I have
> attached my p2n and log files.

R.E.D. is blocked if you run it as superuser or 'root'. In general you
should never run a program as the superuser. Better creating a regular
login and use R.E.D. in this login... If you do want to use R.E.D. as
root just comment the lines 66 - 69 (RED III.52) in the source code
(lines repoted above).

regards, Francois

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Received on Sun Oct 13 2013 - 01:00:02 PDT
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