Dear Sajeewa,
> 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.
ok so you need to install Cygwin (just install all the packages), and
read the docuemntation written by T. Patko:
see
http://q4md-forcefieldtools.org/RED/RED-III.x-Win.pdf
> 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?
I would first use R.E.D. and not X R.E.D.
(X RED is executed using wish)
If you use R.E.D. you need to edit the source code at the very end of
the code (this will change with R.E.D. Python).
See also: http://q4md-forcefieldtools.org/RED/RED-II.pdf
&
http://q4md-forcefieldtools.org/RED/HowTo-III.5.pdf
regards, Francois
> 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 - 07:30:02 PDT
