prepare


SYNOPSIS

prepare  type={{{{QM_ELE | QM_DEN} [theory={HF | DFT; defaults to HF}]  \
    [basis_set={STO-3G | 3-21G | 6-31G | 6-311G | SV | SVP | TZVP | EMSL_3-21G | EMSL_6-311G | EMSL_6-311Gxx; defaults to 6-31G}]   \
    [spin={U | R; defaults to R}]  \
    [d_func=<number of d functions; defaults to 1>]  \
    [p_func=<number of p functions; defaults to 0>]  \
    [f_func=<number of f functions; defaults to 0>]  \
    [diff_sp={YES | NO; defaults to NO}]}  \
    | CS3D [basis_set={SVP | TZVP; defaults to SVP}]  \
    [delsig=<σ-interval compression coefficient; defaults to 6>]  \
    [compress={GZIP | ZIP | NONE; defaults to GZIP}]  \
    [qm_dir=<QM I/O dir; defaults to the directory from which structures were imported>]  \
    | SYBYL file=<.rgn file to be generated>  \
    | MOE_GRID file=<.svl file to be generated>}


DESCRIPTION

The prepare keyword allows preparing input files for 3rd party programs such as GAUSSIAN, FIREFLY, GAMESS-US, TURBOMOLE, COSMOsar3D, MOLDEN, SYBYL, MOE.
If type is set to QM_DEN or QM_ELE, an input file is prepared for each of the currently loaded objects according to the format which characterizes the QM package chosen through the O3_QM_ENGINE environment variable or the env qm_engine keyword; please refer to the calc_field keyword documentation for a description of the various parameters.
If type is set to CS3D, an input file is prepared for each of the currently loaded objects in TURBOMOLE format to carry out the COSMO calculations required by COSMOsar3D to generate the local σ profiles (LSP); additionally, an input file is generated for COSMOsar3D itself with the same grid settings currently loaded in Open3DQSAR.
The input files generated by prepare may then be customized according to the user's specific needs, or for example submitted to a queueing middleware such as PBS. If you do not have the necessity to customize the input files or submit them on a batch queueing system, then it is advisable to use the calc_field keyword instead of prepare to automatically run the computational tasks on your local machine. When O3_QM_ENGINE=molden, the MOLDEN input file is put inside a directory and characterized by the .mdninp extension. The reason why it is put inside a subdirectory is that MOLDEN writes a cube file with electron density or electrostatic potential (according to whether the type is set to QM_DEN or QM_ELE) named "3dgridfile". Creating an individual directory for each MOLDEN computation prevents accidental overwriting of the cube files previously generated.
In summary, prepare should be used only when manual customization of the input files is necessary, or in case submission of the computational tasks has to be carried out on a job queueing system.

If type=SYBYL, followed by file=<region filename>, a .rgn grid definition file is generated like the following:

Filename:  comfagrid.rgn
Created.:  Thu Jun 10 13:46:47 2010

Points:  11088
Boxes:  1

  Box 1            _____ X _____  _____ Y _____  _____ Z _____
  Lower Corner:        12.000000      24.000000      23.000000
  High Corner.:        33.000000      44.000000      46.000000
  Step Size...:         1.000000       1.000000       1.000000
  Number steps:               22               21               24
  Probe Atom..:  C.3
  Charge......:  1.000000


This file (whose filename should contain only alphanumeric characters) is ready to be imported into SYBYL to compute CoMFA fields consistent with the grid settings defined in Open3DQSAR.

Subsequently, the extract_comfa.spl and extract_comsia.spl scripts included in the Open3DQSAR distribution will allow to export CoMFA/CoMSIA data from a SYBYL table as a collection of ASCII files readable by Open3DQSAR using the import type=GRID_ASCII keyword.

If type=MOE_GRID, followed by file=<shape filename>, a .svl shape definition file is generated like the following:

function o3q_define_grid_shape []

return
[
[ -11.0000, -10.0000, -9.0000, -8.0000, -7.0000, -6.0000, -5.0000, -4.0000, -3.0000, -2.0000, -1.0000, 0.0000, 1.0000, 2.0000, 3.0000, 4.0000, 5.0000, 6.0000, 7.0000, 8.0000, 9.0000, 10.0000, 11.0000, 12.0000, 13.0000, 14.0000, 15.0000, 16.0000 ],
[ -16.0000, -15.0000, -14.0000, -13.0000, -12.0000, -11.0000, -10.0000, -9.0000, -8.0000, -7.0000, -6.0000, -5.0000, -4.0000, -3.0000, -2.0000, -1.0000, 0.0000, 1.0000, 2.0000, 3.0000, 4.0000, 5.0000, 6.0000, 7.0000, 8.0000, 9.0000, 10.0000, 11.0000, 12.0000, 13.0000, 14.0000 ],
[ -11.0000, -10.0000, -9.0000, -8.0000, -7.0000, -6.0000, -5.0000, -4.0000, -3.0000, -2.0000, -1.0000, 0.0000, 1.0000, 2.0000, 3.0000, 4.0000, 5.0000, 6.0000, 7.0000, 8.0000, 9.0000, 10.0000, 11.0000, 12.0000, 13.0000 ]
];

endfunction


This file is ready to be used by the WriteMOEGRID.svl script within MOE to compute grid interaction fields consistent with the grid settings defined in Open3DQSAR.
The WriteMOEGRID.svl script included in the Open3DQSAR distribution allows exporting grid interaction field data as a collection of .mgd files in MOE grid format readable by Open3DQSAR using the import type=MOE_GRID keyword.

EXAMPLES

# the following commands allow preparing all the input files necessary to compute a QM electrostatic field using the FIREFLY QM engine using a DFT/RB3LYP level of theory, with a 6-31G(d) basis_set
env  qm_engine=/software/firefly_71g_linux_mpich_p4/firefly
prepare  type=QM_ELE  theory=DFT  basis_set=6-31G  d_func=1

# the following command allows preparing a .rgn region file ready to be imported into SYBYL to calculate CoMFA fields
prepare  type=SYBYL  file=comfagrid.rgn

# the following command allows preparing a .svl shape file ready to be imported into MOE to calculate grid interaction fields
prepare  type=MOE_GRID  file=moegrid.svl

Sitemap
Print version
Contact
Mailing list


Last update:
May 31. 2015 20:39:42

Powered by
CMSimple - CMSimple-Styles


Get Open3DGRID at SourceForge.net. Fast, secure and Free Open Source software downloads



Would you like to align your
dataset? Try Open3DALIGN
Just wish to compute a MIF?
Try Open3DGRID