-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of FyD
Sent: Friday, June 19, 2009 12:19 PM
To: AMBER Mailing List
Cc: q4md-fft.q4md-forcefieldtools.org
Subject: Re: [AMBER] RED Geometry Calculation Error
Francois,
>> When I tried to run the tutorial file and my own p2n file, I kept
>> getting the same error.
>You should 1st try the test cases provided in the R.E.D. tools distribution.
Sorry, Those were the cases I tried (from the tutorial).
>> Geometry optimization(s) is/are being computed for molecule 1 ...
>> [FAILED} See the file(s) "JOB1-gam_m1-1.log"
>Here, this means the optimization step did not finish correctly.
>Check the JOB1-gam_m1-1.log file...
>> I tried searching for the .log file and couldn't find it, checked
>> all my links.
>JOB1-gam_m1-1.log should be in the working directory with the RED code & the P2N file.
>If you do not find JOB1-gam_m1-1.log this might simply mean it was not generated ;-)
>> My "MAIN PROGRAM" is listed below from RED-vIII.2.pl is listed below.
>If I look below, you use Cygwin. right ? I never used R.E.D. on cygwin.
>We have only Linux machines in the lab.
>R.E.D.-III.2 works now on MacOS as well thanks to T. Patko.
>I would first run PC-GAMESS without R.E.D. to see if PC-GAMESS works:
>Using the input "JOB1-gam_m1-1.inp" (generated by R.E.D.) do you get the PC-GAMESS >>output JOB1-gam_m1-1.log ?
They work as long as I change the name of my file to INPUT. It won't recognize the variable "INPUT" even when I define it in system variables. I think the problem is that simply the files cannot be recognized due to issues establishing variables (which seems to be a major issue with CYGWIN). Is there a way to manually perform the process: by that I mean determine the fields directly through PCGAMESS and then have them convert them to .mol2 files to be used with AMBER?
Regards,
Mike
> $XRED = "Off"; # If XRED="ON", R.E.D. will be
> executed using the XRED graphical interface
>
> $NP = "1"; # Number of processor(s) used in
> parallel in QM calculations; useful only if XRED="OFF".
> $QMSOFT = "PC-GAMESS"; # "GAMESS-US", "PC-GAMESS", or
> "GAUSSIAN" (g03, g98 or g94) is used in QM calculations; useful only
> if XRED="OFF".
> # The
> latest Gaussian version detected is used...
> $DIR =
> "/cygdrive/c/Cygwin/mike/RED-III.2-Tools-Files/OUTPUTFILES";
> # Directory name where the final data will be stored; useful only if
> XRED="OFF".
>
> $OPT_Calc = "On"; # Geometry optimization will be
> carried out only if $OPT_Calc = "ON"; useful only if XRED="OFF".
> $MEPCHR_Calc = "On"; # MEP computation & charge fitting
> will be carried out if $MEPCHR_Calc = "ON"; useful only if XRED="OFF".
>
> $CHR_TYP = "RESP-A1"; # Charge derivation models:
> "RESP-A1, RESP-A2, RESP-C1, RESP-C2, ESP-A1, ESP-A2, ESP-C1,
> ESP-C2"; useful only if XRED="OFF".
> # -1- RESP-A1: HF/6-31G* Connolly
> surface algo., 2 stage RESP fit qwt=.0005/.001
> # -2- RESP-A2: HF/6-31G* Connolly
> surface algo., 1 stage RESP fit qwt=.01
> # -3- RESP-C1: HF/6-31G* CHELPG
> algo., 2 stage RESP fit qwt=.0005/.001
> # -4- RESP-C2: HF/6-31G* CHELPG
> algo., 1 stage RESP fit qwt=.01
> # -5- ESP-A1: HF/6-31G* Connolly
> surface algo., 1 stage RESP fit qwt=.0000
> # -6- ESP-A2: HF/STO-3G Connolly
> surface algo., 1 stage RESP fit qwt=.0000
> # -7- ESP-C1: HF/6-31G* CHELPG
> algo., 1 stage RESP fit qwt=.0000
> # -8- ESP-C2: HF/STO-3G CHELPG
> algo., 1 stage RESP fit qwt=.0000
> # -9- DEBUG: Do not use the DEBUG
> mode for generating correct charge values !!!
> # The DEBUG mode can be used to (i)
> quickly get an idea of "what is done", (ii) debug the source code &
> (iii) create new functionalities.
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Received on Mon Jul 06 2009 - 10:11:02 PDT
