Dear Francois,
Thank you. i will follow you.
On Fri, Sep 7, 2012 at 2:49 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Quoting shomesankar bhunia <rightclickatrighttime.gmail.com>:
>
> > GAMESS is working fine now. I have to follow your
> > instructions regarding RESP.Thanks again.
>
> Still to start:
> A key point is to understand the 2 types of atom names in the P2N files:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#RULES
> -> automatic generation of the inputs for the RESP program
>
> In short, better use Ante_R.E.D. 2.0 at R.E.D. Server than Ante_R.E.D.
> 1.x in the R.E.D. tools III.x
> See http://q4md-forcefieldtools.org/REDS/news.php
> http://q4md-forcefieldtools.org/REDS/news.php#2
>
> regards, Francois
>
>
> > On Fri, Sep 7, 2012 at 11:50 AM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Dear Shomesankar Bhunia,
> >>
> >> > I set the scratch directory to /temp. And you are perfectly right
> >> that i
> >> > am getting a *.inp file and a blank *.log file. I tested the command
> sent
> >> > by you .the log output is again an empty file and the terminal output
> is
> >> as
> >> > below . it is giving "set:Syntax Error". thanks in advance
> >>
> >> So it means the GAMESS program is not correctly installed...
> >>
> >> You need to correctly install the GAMESS and RESP programs before to
> >> execute R.E.D.
> >>
> >> > ubuntu:~/RED/RED-III.51-Tools-Files/working_dir_acetate/red> rungms
> >> > JOB2-gam_m1-1-1 00 1 > JOB2-gam_m1-1-1.log
> >> > set: Syntax Error.
> >> > ubuntu:~/RED/RED-III.51-Tools-Files/working_dir_acetate/red>
> >>
> >> "set: Syntax Error."
> >> -> this is a csh error.
> >> -> I guess this means you introduced an error in the 'rungms'
> script...
> >>
> >> When using R.E.D.:
> >> - always test Gaussian, GAMESS or Firefly in a standalone mode; i.e.
> >> without R.E.D. before executing R.E.D.
> >> - run also the RESP program in a standalone mode (simply type the
> >> 'resp' command in a terminal); you should get:
> >> usage: resp [-O] -i input -o output -p punch -q qin -t qout -e
> >> espot -w qwts -s esout
> >> - Then, when executing R.E.D. for the first time; set $CHR_TYP = "DEBUG"
> >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
> >> thus system errors printed in the console will be displayed (while
> >> when using $CHR_TYP = "RESP-A1" these errors and other unwanted
> >> messages generated by the interfaced programs are hidden).
> >>
> >> regards, Francois
> >>
> >>
> >> > On Thu, Sep 6, 2012 at 2:48 PM, FyD <fyd.q4md-forcefieldtools.org>
> >> wrote:
> >> >
> >> >> Dear Shomesankar Bhunia,
> >> >>
> >> >> R.E.D. reports:
> >> >> The Scratch directory defined for GAMESS is .
> >> >> -> this is a strange idea ;-) We never tested '.' as a scratch
> >> >> directory...
> >> >> Could try to set the scratch directory as /tmp in 'rungms'?
> >> >>
> >> >> > yes i looked at the "JOB2-gam_m1-1-(X).log" file but it is blank.
> >> So i
> >> >> > have no idea where the problem is.Thanks in advance
> >> >>
> >> >> R.E.D. executes the following command:
> >> >> $rungms JOB2-gam_m$NM-$NC-$w $gx $NP > JOB2-gam_m$NM-$NC-$w.log
> >> >>
> >> >> $NM = molecule number
> >> >> $NC = conformation number for the molecule
> >> >> $w = orientation number for the conformation
> >> >> $gx = integer between 00 and 09 corresponding to the gamess.$gx.x
> >> binary
> >> >> $NP = number of processors used in a SMP system
> >> >>
> >> >> When you executed R.E.D. the JOB2-gam_m1-1-1.inp file was generated
> >> >> and the JOB2-gam_m1-1-1.log output is an empty file if I understand
> you.
> >> >>
> >> >> In the console where you ran R.E.D.: manually execute (1 core is
> used):
> >> >> rungms JOB2-gam_m1-1-1 00 1 > JOB2-gam_m1-1-1.log
> >> >> 00 : I guess gamess.00.x is your gamess binary you got after
> >> >> compilation...
> >> >> what do you get in the terminal? in the JOB2-gam_m1-1-1.log output
> file?
> >> >> same question with (2 cores are used this time):
> >> >> rungms JOB2-gam_m1-1-1 00 2 > JOB2-gam_m1-1-1.log
> >> >>
> >> >> regards, Francois
> >> >>
> >> >>
> >> >> > On Thu, Sep 6, 2012 at 9:00 AM, Marc van der Kamp
> >> >> > <marcvanderkamp.gmail.com>wrote:
> >> >> >
> >> >> >> Hi,
> >> >> >>
> >> >> >> I'm sure FyD will reply at some point, but it would be more
> useful to
> >> >> show
> >> >> >> what error JOB2-gam_m1-1-(X).log shows, as your output says:
> >> >> >>
> >> >> >> See the file(s) "JOB2-gam_m1-1-(X).log"
> >> >> >>
> >> >> >> Have you looked at that?
> >> >> >>
> >> >> >> --Marc
> >> >> >>
> >> >> >> On 6 September 2012 13:57, shomesankar bhunia <
> >> >> >> rightclickatrighttime.gmail.com> wrote:
> >> >> >>
> >> >> >> > Hii
> >> >> >> > I am trying to calculate the RESP charges using RED-vIII.5.
> tools.
> >> >> but i
> >> >> >> > am getting the following error. what I have to do. Thanks in
> >> advance.
> >> >> >> >
> >> >> >> >
> >> >> >> > * Selected optimization output *
> >> >> >> > GAMESS
> >> >> >> > Optimization OUTPUT looks nice !
> >> >> >> >
> >> >> >> > * 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 GAMESS
> Algorithm!
> >> >> >> >
> >> >> >> > * Selected QM Software *
> >> >> >> > GAMESS
> >> >> >> >
> >> >> >> > * Software checking *
> >> >> >> > gamess.00.x [ OK ]
> >> >> >> > rungms [ OK ]
> >> >> >> > ddikick.x [ OK ]
> >> >> >> > resp [ OK ]
> >> >> >> >
> >> >> >> > The Scratch directory defined for GAMESS is .
> >> >> >> >
> >> >> >> > Scratch directory for GAMESS [ OK ]
> >> >> >> >
> >> >> >> > The punch file directory defined for GAMESS is $SCR/$JOB.dat
> >> >> >> >
> >> >> >> > MEP(s) is/are being computed for molecule 1 ... [ FAILED ]
> >> >> >> > See the file(s) "JOB2-gam_m1-1-(X).log"
>
>
>
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Received on Fri Sep 07 2012 - 00:30:02 PDT
