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 - 00:00:05 PDT
