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 Tue Oct 15 2013 - 22:30:02 PDT
