Hi Francois,
My operating system is windows 7. I know we usually run these in linux and
mac but as it also said in the website that I could run on windows systems
I ran it in my laptop which had windows 7.
I haven't programmed in perl but I can kind of undestand where to set the
value of a variable. In the perl script RED-v_3.5.pl I cannot clearly see a
place where it allows me to set the value of the variable $OPT_Calc. I
noticed the following piece of code
$XRED =~ s/^\s*(.*?)\s*$/$1/; $XRED = uc($XRED);
if(($XRED ne "ON") && ($XRED ne "OFF")){ $XRED = "OFF" }
if($XRED eq "ON"){
$i=0;
if (-e "./RED.cfg"){
open(CFG,"<RED.cfg");
foreach (<CFG>){
if(!/#/ig){
if($i==0){ $QMSOFT=$_; chomp($QMSOFT); }
if($i==1){ $OPT_Calc=$_; chomp($OPT_Calc); }
if($i==2){ $MEPCHR_Calc=$_; chomp($MEPCHR_Calc); }
if($i==3){ $Re_Fit=$_; chomp($Re_Fit); }
if($i==4){ $CHR_TYP=$_; chomp($CHR_TYP); }
if($i==5){ $DIR=$_; chomp($DIR); }
if($i==6){ $NP=$_; chomp($NP); }
if($i==7){ $COR_CHR=$_; chomp($COR_CHR); }
$i++;
}
}
close(CFG);
}
XTerminal();
}
As you can see it says if($i==1){ $OPT_Calc=$_; So where shall I change
this value of "i"? It also mentions loading the settings from RED.cfg.
Iooked into that as well. It doesn't clearly specify anything as well. It
looks like below.
# X R.E.D. CONFIG. File
# ----------------------------
# PART 1 QM Software
FIREFLY
# ----------------------------
# PART 2 Tasks performed
OFF
OFF
OFF
# ----------------------------
# PART 3 Charge model
RESP-A1
# ----------------------------
# PART 4 Directory
Data-RED
# ----------------------------
# PART 5 Processor number
1
# -----------------------------
# PART 6 Charge accuracy
4
# -----------------------------
# END
So where exactly do I specify the $i or $OPT_Calc in the perl script. I am
kind of a little confused at the moment. Could you please help me out?
Thank you
Sajeewa
On Sun, Oct 13, 2013 at 3:45 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Sajeewa Pemasinghe,
>
> > This is the first time I am using RED tools. I am following the tutorial.
> >
> > I ran the Ante_RED-1.5.pl on my pdb and got the corresponding p2n file.
>
> See http://q4md-forcefieldtools.org/REDS/news.php#2
> 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 Ante_RED-1.5.pl. I renamed the p2n file as Mol_red1.p2n and
> > the gaussian log file as Mol_red1.log and ran the RED-v3.5.pl.
>
> this is correct; this means you use
> $OPT_Calc = "Off" & $MEPCHR_Calc = "On"
>
> you could also use $OPT_Calc = "On" & $MEPCHR_Calc = "On" and provide
> only the P2n file(s) as input(s)
>
> see http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
>
> > I get the message
> >
> > 'uname' is not recognized as an internal or external command,
> > operable program or batch file.
>
> there is something wrong... Which operating system do you use?
>
>
> > * Operating system *
> >
> > ERROR: DO NOT RUN THIS SCRIPT AS ROOT !
>
>
> You can find in the source code:
>
> if($<==0){
> print "\n\t\tERROR: DO NOT RUN THIS SCRIPT AS ROOT !\n\n"; $check=0;
> Information();
> if($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 - 06:00:04 PDT
