Dear Francois,
I am now running RED tools on Ubuntu. To do the optimization I used the
gaussian input file created by the Ante_RED-1.5.pl. That input file has "
#P hf/6-31G* Opt=(Tight,CalcFC) Freq SCF(Conver=8) Test" as keywords. Then
using the log file generated by gaussian and the p2n file generated by
Ante_RED-1.5.pl I ran RED-v3.5.pl and it gives me the following error.
* Selected optimization output *
GAUSSIAN
Invalid optimization OUTPUT !
A frequency job is found after the geometry optimization
You need to remove this frequency job from the Gaussian output
According to the keywords used by the Ante_RED generated input file, a
frequency calculation is done. Should I just remove the 'freq' keyword and
do the optimization and then run RED or is there something else I need to
know?
Thank you
Sajeewa
On Sun, Oct 13, 2013 at 10:02 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Tue Oct 15 2013 - 14:30:03 PDT
