Dear Francois
You are absolutely right. I have a problem with LEAP and according to
your suggestions it has been solved. There is no problem regarding COORD=
CART. Thanks for the support.
On Sun, Sep 16, 2012 at 3:54 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Shomesankar Bhunia,
>
> > 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.
>
> The warning you reported is about using COORD=CART in GAMESS.
> There are some explanations about COORD=CART vs COORD=UNIQUE at:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
> see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/#S7title
> the part related "Charge reproducibility"
>
> or see the GAMESS manual ;-)
>
> > I next used the mol2 file in AMBER ... ANTECHAMBER package
> > to develop the .prmtop and .inpcrd files for the ligand.
>
> You could use Antechamber to add the atom types or these atom types
> could be added using a LEaP script (see the 'set' command for instance
> at http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff).
> prmtop/prmcrd files are generated with the LEaP program once again.
>
> > The main problem
> > is when i transferred the .prmtop and .inpcrd files of the ligand in VMD
> it
> > is displaced from the protein site.
>
> if I understand you your ligand for which you have generated a new FF
> library is embedded in a protein.
>
> > Its staying out from the protein
> > binding cavity.A change in coordinate has occured for the ligand.
>
> oh oh something wrong here...
>
> You need to load in LEaP the force field (FF) of your choice in LEaP
> with the corresponding FF libraries and your new FF library for your
> ligand. Then you load in LEaP your PDB file that contains the ligand
> in the protein (i.e. often an experimental structure from the protein
> data bank); you define the solvation conditions and the counter ions
> if needed. At the end when you create the prmtop/prmcrd files the
> Cart. coordinates will be taken from the PDB file, while the charges &
> FF atom types will come from the FF libraries. Thus, the Cart.
> coordinates in the FF libraries do NOT matter.
>
> > I have
> > again submitted a GAMESS job using COORD=UNIQUE.
>
> If you choose the rigid body-reorientation algorithm in R.E.D. it does
> not matter.
>
> > I didnt get a WARNING this time.
>
> this is normal because COORD=CART is not used.
>
> > I have to see what happens after the job is complete.
>
> This will change nothing for the problem you reported above. I think
> the way you use the FF libraries in LEaP is wrong: the Cart.
> coordinates in the FF libraries do NOT matter.
>
> > 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.
>
> ok in another email.
>
> regards, Francois
>
>
> > 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 Sun Sep 16 2012 - 21:30:03 PDT
