Dear Dongshan,
> Did you meet one problem "ERROR: Problem with the QM Scratch directory"
> when using R.E.D. VIII.52 to derive the charge of atoms? In my case, I had
> used gamess to optimized the molecular structure and when I executed R.E.D.
> VIII.52 with "perl RED-vIII.5.pl" command, the error is always showing as
> follows:
which GAMESS do you interface?
> The Scratch directory defined for GAMESS is /local_scratch/$USER
>
> Scratch directory for GAMESS [ NOT FOUND ]
So you need to create the corresponding scratch directory before to
execute R.E.D.
> The USER Scratch directory defined for GAMESS is /scratch/$USER
> Bad permissions for the GAMESS Scratch directory
'chmod 777' for this scratch directory...
> The punch file directory defined for GAMESS is $USERSCR/$JOB.dat
>
> ERROR: Problem with the QM Scratch directory.
> See the R.E.D.-II manual, page 7.
See
http://q4md-forcefieldtools.org/RED/RED-II.pdf
> About the above error, I have some questions to ask:
> (1) To execute R.E.D.VIII.52, how many input files need to be read? I think
> the necessary files are only three: Mol-red1.p2n, Mol-red1.log and
> Mol-red1.dat. Is this correct?
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
- if $OPT_Calc = "On" & $MEPCHR_Calc = "On" only the P2N file(s)
is(are) required; i.e. in your case Mol_red1.p2n
- if $OPT_Calc = "Off" & $MEPCHR_Calc = "On" the P2N file(s) and QM
output log file(s) are required; i.e. in your case Mol_red1.p2n &
Mol_red1.log
I do not know what is this Mol_red1.dat file; I think you mix up the
punch file and that Mol_red1.dat file.
See
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
&
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/figure/F1/
the punch file is the JOB2-gam_m$n-$i-$j.dat file
$n molecule // $i conformation // $j orientation
> (2) To my understanding, the scratch directory /local_scratch/$USER is
> generated temporarily for intermediate outputs during the optimization
> calculation before executing R.E.D. fitting, and after the job is finished,
> the temporal scratch directory will be deleted automaticly. So to do R.E.D.
> fitting, the scratch directory is not necessary. Is this correct?
on a cluster - & using the PBS queuing system, Yes, a temporary
scratch directory can be created just before executing R.E.D. and
removed just after the job has finished.
on a workstation you could create this scratch directory only once and
keep it for all the R.E.D. jobs... If this scratch directory is only
for your login you could use a specific directory in your login (if
you have a enough space in your login also)
If the scratch directory is to be shared with other users you could
use the /tmp partition and then create a directory in /tmp related to
your login. /tmp could be a particular partition with a looot of room.
> (3) From the above information, it seems the R.E.D. VIII.52 cannot
> recognize variables such as $USER, $USERSCR, $JOB, because the directory
> /scratch/dswei and the file /scratch/dswei/Mol-red1.dat do exist. Here
> dswei is my username on the cluster. How to solve the problem?
please tell me which GAMESS version you use? and send me your 'rungms'
script: I could prepare it for you if you agree...
> I'm learning the R.E.D., so your reply to my above question will be great
> help to me.
do not hesitate to ask as many questions as you wish ;-)
regards, Francois
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Received on Mon Sep 30 2013 - 13:30:09 PDT
