Dear Francois,
I gave up to use the cluster to execute RED charge fitting and changed to
use the RED server on your website. Now I can finish the charge fitting
task and get the .mol2 file for Amber using. I notice that the RED server
use RED-III.4 instead of RED-III.52 to execute the charge fitting
procedure. Is there really bugs in RED-III.52 tools?
Anyway, thank you so much for your patient replies to my questions.
Best!
Dongshan
On Tue, Oct 8, 2013 at 11:37 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> Dear Francois,
>
> I'm still having questions about the execution of RED-III.52. When I
> execute the command "perl RED-vIII.5.pl", I got the same question with
> the following link:
> http://q4md-forcefieldtools.org/RED/popup/bugs-III.4.txt
>
> "Problem: The scratch path defined in the "rungms" script of the GAMESS-US
> program is not found by R.E.D.-III.4 if an environment variable such as
> $USER is used in the path. For instance the /tmp/$USER path is not found
> even if the corresponding directory does exist (environment $USER variable
> points to "bill"), while /tmp/bill is found. This leads to the following
> error message: "
>
> So RED-III.52 doesn't update the bug? I want to go back to use RED-III.4,
> but it seems the RESP web doesn't offer the download for RESP-III.4 tools.
> Is it true?
>
> Best!
>
> Dongshan
>
>
> On Tue, Oct 1, 2013 at 1:35 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Dongshan,
>>
>> Do you use the PBS queuing system?
>>
>> At R.E.D. Server we do use PBS (Torque/Maui):
>> See http://q4md-forcefieldtools.org/REDS/faq.php#8
>> We also use the same gamess version...
>>
>> # set SCR=/scr/$USER
>> # set USERSCR=~$USER/scr
>> # set GMSPATH=/u1/mike/gamess
>> set SCR=/tmp/ZZZZZZ
>> set USERSCR=/tmp/ZZZZZZ
>> set GMSPATH=/usr/local/gamess
>>
>> We use the same direction for SCR and GMSPATH; R.E.D. will move the
>> punch file from the scratch directory to the working directory to
>> extract the MEP...
>>
>> and the PBS script modify rungms to create a unique & temporary
>> scratch directory by job:
>> see and example:
>> set SCR=/tmp/R.E.D.IV-4379.master0.q4md-forcefieldtools.org
>> set USERSCR=/tmp/R.E.D.IV-4379.master0.q4md-forcefieldtools.org
>> set GMSPATH=/usr/local/gamess
>>
>> ---
>>
>> the definition of the punch file is done in the script gms-files.csh
>> setenv INPUT $SCR/$JOB.F05
>> setenv PUNCH $USERSCR/$JOB.dat
>> setenv AOINTS $SCR/$JOB.F08
>> setenv MOINTS $SCR/$JOB.F09
>> setenv DICTNRY $SCR/$JOB.F10
>>
>> regards, Francois
>>
>>
>> > Thanks for your detailed reply. The gamess I used on the cluster is
>> gamess
>> > 5.1.2012 version. The rungms script is original from the gamess software
>> > and is attached here. Please help me have a look.
>> >
>> > Especially, the scratch directory /local_scratch/dswei disappeares after
>> > the job running finishes. I tried to change the scratch directory to my
>> > user directory in the rungms script and submitted a job to the cluster,
>> but
>> > the job quit quickly since there is no comminucation between the node
>> and
>> > my user directory. So how can I create a scratch directory both for job
>> > running and output saving?
>>
>> > On Tue, Oct 1, 2013 at 4:07 AM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>> >
>> >> 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
>> >>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ---------------------------------------------------------
> Dongshan Wei, Dr.
> Chongqing Institute of Green and Intelligent Technology, CAS
> 85 Jinyu Ave, Yubei Area, Chongqing 401120, China
> Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
> Phone: (+86) 23-63063762
> ---------------------------------------------------------
>
--
---------------------------------------------------------
Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
85 Jinyu Ave, Yubei Area, Chongqing 401120, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-63063762
---------------------------------------------------------
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Received on Tue Oct 08 2013 - 21:00:03 PDT
