Not in Amber9 manual. As you mention below, I saw TEMPK in divcon.out and what
you say below is very likely the case.
I have killed that procedure with antechamber, started more plain MD, while
considering the use of DivCon for the big molecule. Surely I am being
considered an intruder, attempting to do with amber what Amber was not
conceived for. However, except MD, I can't see any other approach to treat
these big molecules. More importantly, these molecules feature extremely
interesting interactions with receptors, and that is my final goal.
Reading Divcon 4.5 manual it becomes clear what could have not been otherwise:
linear scaling implies residues. I learned how to set residues for non
polymeric natural products in the world of NWChem and perhaps the finished
examples are still somewhere in my machines. As soon as the "plain" MD alluded
to above is over, I'll try DivCon with them, as a preliminary for my big
molecule. It is not yet fully clear to me how DivCon can be used as standalone
in the context of Antechamber, though I imagine that is not the divcon.out file
itself to be used, rather, in some way, the AM1BCC. ac and orep.ac files that
should also be produced by divcon.
I believe I fully understand you skepticism about getting and using for MD AM1
charges obtained for a big single residue. May be the way divcon works on
linear scaling makes things more palatable.
francesco pietra
ADDITIONAL(DEFAULT) KEYWORDS ------------------
------------------------------------------------------------------------------
ECRIT=4.0E-06 - CONVERGENCE CRITERION FOR ENERGY
DCRIT=5.0E-04 - CONVERGENCE CRITERION FOR DMX (DENSITY MATRIX)
MAXIT=100 - MAXIMUM NUMBER OF SCF ITERATIONS ALLOWED
TEMPK=1000.0 - A D&C TEMPERATURE REQUESTED
ADDMM - ADD MM CORRECTION TO PEPTIDE TORSIONAL BARRIER
RMIN=0.5 - MIMIMUM DISTANCE ALLOWED BETWEEN ATOMS
INTGLS=TALMAN - TALMAN INTEGRALS TO BE USED
NOXML - DO NOT GENERATE AN XML FILE
MAXOPT=0 - MAXIMUM NUMBER OF GEOMETRY OPTIMIZATION CYCLES; IT IS
TEN TIMES THE NUMBER OF SOME GEOMETRICAL PARAMETERS
ETEST=2.0E-03 - GEOMETRY OPTIMIZATION ENERGY CHANGE CRITERION
GTEST=5.0E-01 - GEOMETRY OPTIMIZATION GRADIENT COMPONENT CRITERION
DIIS - USE DIIS METHOD IN BFGS GEOMETRY OPTIMIZATION
--- "David A. Case" <case.scripps.edu> wrote:
> On Wed, Aug 15, 2007, Francesco Pietra wrote:
>
> > I was mislead by the temperature setting, that Amber9 manual lists under
> the
> > "divide and conquer" option.
>
> Can you be more explicit about where this is? I've looked for it, to try to
> change it, but I seem to be missing where in the Amber manual.
>
> I'm guessing maybe you thought the divcon.out file is ambiguous, since it
> says
> both "standard calculation (no d&c)" and "d&c temperature of 1000 K will be
> used". The latter is under "defaults", but should probably not be printed if
> "standard" is set. If that is it, then the divcon people read this list, and
> can fix the problem in future versions.
>
> ...thx...dac
>
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Received on Sun Aug 19 2007 - 06:07:27 PDT
