AMBER Archive (2008)

Subject: Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Dec 12 2008 - 12:24:25 CST

Hi Stephane,

> I have changed the name of the files and the program start but also
> stops immediately with the message
>
> ---------------------------
> * Welcome to R.E.D. III *
> RESP ESP charge Derive
> http://q4md-forcefieldtools.org/RED/
>
> CHARGE TYPE = RESP-A1
> ---------------------------
>
> ===========================================================================
> ======================= Single molecule ===========================
> The molecule TITLE is "Acetate"
> The TOTAL CHARGE value of the molecule is "-1"
> The SPIN MULTIPLICITY value of the molecule is "1"
> ===========================================================================
>
> * Selected optimization output *
> GAUSSIAN
> Invalid optimization OUTPUT !
>
> the log file came from gaussian 03.
>
> I have also changed the variable $OPT_Calc = "On" to "Off". If i
> keep $OPT_Calc = "On", i obtained the error message

Do you have a frequency job in your Acetate job ?
(or do the Acetate QM job without the "Freq" keyword)
If yes, just remove it...
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#6

It is written:
"It is always a good idea to look for negative frequencies in a
geometry optimization output (this is a common problem when partial
optimizations are carried out with geometric constraints). This can be
done using the following UNIX command:
[fyd_at_lynx 2-Geom-Opt]$ grep "Frequencies" AIB-Conf*-Gaussian.log"

& then in section:
   -4- The last step consists of checking and preparing the P2N and QM
output files for the R.E.D. III execution:

Finally, the frequency job available in the Gaussian output has to be
removed from the QM output (R.E.D. II and III only recognize
optimization output, and generates an error message if an optimization
job followed by frequency calculations is used as input; this might be
changed in R.E.D. IV).

This part of the code is not very smart...

> ---------------------------
> * Welcome to R.E.D. III *
> RESP ESP charge Derive
> http://q4md-forcefieldtools.org/RED/
>
> CHARGE TYPE = RESP-A1
> ---------------------------
>
> ===========================================================================
> ======================= Single molecule ===========================
> The molecule TITLE is "Acetate"
> The TOTAL CHARGE value of the molecule is "-1"
> The SPIN MULTIPLICITY value of the molecule is "1"
> ===========================================================================
>
> * 1 conformation(s) selected *
>
> WARNING:
> A 2nd column of atom names is detected
> This 2nd column will be used in the PDB (& Tripos) file(s)
>
> WARNING:
> No three atom based re-orientation found in the P2N file
> Re-orientation will be done according to the GAUSSIAN Algorithm!
>
> * Selected QM Software *
> GAUSSIAN
>
> * Software checking *
> gaussian [ NOT FOUND ]
> resp [ NOT FOUND ]
>
> what is wrong ?

You need to set up your .bashrc file if you use bash shell or .cshrc
if you use tcsh/csh.

Here is a part of my .cshrc:
------------------------------------------
setenv SOFT /usr/local
setenv AMBERHOME /usr/local/amber10

setenv GAMESS_SCR /Big-disk/0QM_SCR
setenv GAUSS_SCRDIR /Big-disk/0QM_SCR
setenv g03root /usr/local
source /usr/local/g03/bsd/g03.login
set path = ($path $AMBERHOME/exe $SOFT/g03 $SOFT/gamess $SOFT/firefly)

------------------------------------------

If I use the "which" UNIX command, I get:

[fyd_at_lynx ~]$ which g03
/usr/local/g03/g03
[fyd_at_lynx ~]$ which resp
/usr/local/amber8/exe/resp

regards, Francois

PS
CEA-Saclay is South of Paris: you can come in Amiens anytime if you wish ;-)

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