Dear Francois,
I have generated the GAMESS log file (after the warning the job
is running fine) and derived the RESP charge using RED tools and generated
the mol2 file. I next used the mol2 file in AMBER ... ANTECHAMBER package
to develop the .prmtop and .inpcrd files for the ligand. The main problem
is when i transferred the .prmtop and .inpcrd files of the ligand in VMD it
is displaced from the protein site. Its staying out from the protein
binding cavity.A change in coordinate has occured for the ligand. I have
again submitted a GAMESS job using COORD=UNIQUE. I didnt get a WARNING
this time. I have to see what happens after the job is complete. I have
another problem although i have four cpu workstation i cant distribute the
job in four cpus, instead it is running in one cpu. I searched and tried a
lot by changing NCPU== 4 and setting hostname to localhost, but the same
message" i dont know how to run the job in parallel" is coming. Can you
please help me out? Thanks in advance.
On Sat, Sep 15, 2012 at 6:30 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Shomesankar Bhunia,
>
> A warning is not an error message...
> What do you get _after_ this warning? there is nothing wrong with this
> warning...
>
> regards, Francois
>
>
> > I want to generate RESP charge of raloxifene. I have generated a GAMESS
> > input using the RED-tools for which i am getting a warning while running
> > gamess. my inputs are mentioned below. i think the coordinates of my
> > molecule are changed. Is that so? thanks in advance
>
> [...]
>
>
> > * * * WARNING * * *
> > OLD KEYWORD COORD=CART SELECTED, AUTOMATICALLY CHANGED TO
> COORD=PRINAXIS.
> > YOUR MOLECULE'S COORDINATES WILL BE CHANGED TO PRINCIPAL AXES BY
> > A) TRANSLATION TO THE CENTER OF MASS, THEN
> > B) ROTATION TO HAVE A DIAGONAL MOMENT OF INERTIA TENSOR.
> >
> > HOWEVER, NOTHING ELSE IN YOUR INPUT WILL BE ROTATED IN THE SAME WAY,
> > SO IF YOU HAVE A $VEC, $VIB, $GRAD, $HESS, EFP PARTICLE COORDINATES,
> > OR ANYTHING ELSE THAT DEPENDS ON THE INITIAL ORIENTATION, THAT DATA
> > WILL NOT BE USED CORRECTLY IN THIS RUN.
> >
> > THE PURPOSE OF COORD=PRINAXIS IS TO BE USED ONCE, ONLY AT THE VERY
> > BEGINNING OF A SERIES OF COMPUTATIONS, PERHAPS TO FIND THE SYMMETRY
> > UNIQUE ATOMS FROM AN ARBITRARY INITIAL ORIENTATION.
> >
> > AFTER THE FIRST RUN, YOU SHOULD USE ONLY COORD=UNIQUE, TO ENSURE THAT
> > THE COORDINATES WHICH YOU READ IN ARE THE COORDINATES THAT ARE USED.
>
>
>
>
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Received on Sat Sep 15 2012 - 10:30:04 PDT
