Dear Francois,
Thank you very much for your advice. Thanks to your program R.E.D Tools
charge derivations has been much much easier.
Sajeewa
On Wed, Oct 16, 2013 at 1:21 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Sajeewa,
>
> > 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.
>
> pay attention when using Ante_R.E.D. 1.x!
> see http://q4md-forcefieldtools.org/REDS/news.php#2
> Ante_R.E.D. 2.0 vs Ante_R.E.D. 1.x
>
> > * 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?
>
> You could:
> - remove the Freq keyword in the Ante_RED output, run Gaussian and use
> the Gaussian input directly as it is as in input for R.E.D. with the
> P2N file.
> - run Gaussian with the Freq keyword; then save the output with the
> Freq job and remove the Freq job from the output to be used as input
> for RED.
>
> job Opt=Tight Freq
> ...
> geometry optimization
> ...
> Stationary point found
> ...
> Normal termination of Gaussian
> ... !
> frequency job ! part of the output
> ... ! to be removed
> Normal termination of Gaussian ! to be used by RED
>
> all that is defined in the tutorial:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#6
> section -4- line in red color...
>
> all that is fully handled by R.E.D. Python...
>
> regards, Francois
>
>
> > 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 Sun Oct 20 2013 - 09:00:02 PDT
