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 - 01:00:02 PDT
