calc_field


SYNOPSIS

calc_field  type={{MM_ELE [diel_dep={CONST | DIST; defaults to CONST}]  \
    [diel_const=<dielectric constant value; defaults to 1.0>]  \
    | VDW [probe_type=<atom type of the probe; defaults to MMFF94 CR>]}  \
    [smooth_probe={YES | NO; defaults to NO}]     | MD_GRID [probe_type=<GRID probe type; defaults to C3>]  \
    [diel_const=<dielectric constant value; defaults to 80.0>]  \
    [cutoff=<max energy cutoff value in kcal/mol; defaults to 5.0>]  \
    [md_grid_dir=<GRID I/O dir; defaults to the directory from which structures were imported>]  \
    | {{{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>]  \
    [qm_scratch=<QM scratch dir; defaults to the temporary directory>]}  \


DESCRIPTION

The calc_field keyword allows computing molecular interaction fields. Open3DQSAR can calculate Van der Waals and electrostatic fields according to classical molecular mechanics equations using the Merck force field (type=VDW | MM_ELE). Additionally, it can compute COSMOsar3D descriptors [1] if the CS3D program and TURBOMOLE are installed on the system.
It can also drive Molecular Discovery GRID, if it is installed on the system, to calculate MIFs based on GRID force field and probes. Finally, it can compute electrostatic potential and electron density MIFs using ab initio quantum mechanics (type=QM_ELE | QM_DEN). By default, the calc_field module operates in parallel fashion on multiprocessor machines, using all the CPUs available in the system; if one wishes to run the computation on a lower number of CPUs, this may be specified before calling calc_field with the env n_cpus keyword.


MM force-field based MIF computation

As far as molecular mechanics are concerned (type={VDW | MM_ELE}), the Merck force field (MMFF94) is used.
Electrostatic interactions are computed according to Coulomb's law (Equation 1):

        (1)


It is possible to specify the value of the dielectric constant through the diel_const parameter (which defaults to 1.0), and to choose whether to use a constant dielectric (diel_dep=CONST, the default) or a distance-dependent dielectric (diel_dep=DIST).

The expression for Van der Waals in MMFF94 is described by Equation 2:

        (2)

where Rij and εij are defined as follows:










A probe is placed in each node of the currently loaded grid and the Van der Waals (for type=VDW) or electrostatic (for type=MM_ELE) interactions are computed between the probe and each atom of the molecules belonging to the currently loaded dataset. Appropriate atom types, charges and Van der Waals parameters are automatically assigned according to the force-field chosen through the force_field parameter by calling OpenBabel utilities.
If the smooth_probe parameter is set to YES, energy values are computed as the average of the energy in the grid point and the energies in the eight vertexes of a box centred on the grid point; the displacement of vertexes from the centre of the box in each direction is equal to 1/3 of the grid's step size.

Here follows a list of the MMFF94 atom types which may be chosen as probe atoms through the probe_type parameter; the default probe is CR.

MMFF94 probe types

CRAlkyl carbonO+Oxonium (tricoord) O
C=CVinylicHO+H on oxonium oxygen
C=OGeneral carbonyl CO=+Oxenium oxygen+
CSPAcetylenic CHO=+H on oxenium O+
HCH-C=N=N twice double bonded
ORO-CSp3N+=CIminium nitrogen
O=CO=C, genericNCN+ Q=1/2
NRAmine NNGD+ Q=1/3
N=CN=C, iminesCGD+Guanidinium carbon
NC=ON-C=O, amidesNPD+N pyridinium ion
FFluorineOFURAromatic O, furan
CLChlorineC%Isonitrile carbon
BRBromineNR%Isonitrile N
IIodineNMSulfonamide N-
SThiol, sulfideC5AAlpha arom 5-ring C
S=CS doubly bonded to CC5BBeta arom 5-ring C
S=OSulfoxide SN5AAlpha arom 5-ring N
SO2Sulfone SN5BAlpha arom 5-ring N
SISiliconN2OXNitrogen in N-oxide
CR4RC in cyclobutylN3OXNitrogen in N-oxide
HORH-O, alcoholsNPOXNitrogen in N-oxide
CR3RC in cyclopropylOH2Oxygen in water
HNRH-N, aminesHSH-S
HOCOH-O, acidsS2CMThiocarboxylate S
PO4PhosphodiesterSO2MSulfur in sulfinate
PTricoordinate P=S=OSulfinyl sulfur, C=S=O
HN=CImine N-H-P=CP doubly bonded to C
HNCOH-N, amidesN5MNeg N in tetrazole anion
HOCCH-O, enols, phenolsCLO4Chlorine in ClO4(-)
CE4RC=C in 4-ringC5General arom 5-ring C
HOHH-OHN5General arom 5-ring N
O2CMO, Carboxylate anionCIM+C in N-C-N, Im+ ion
HOSH-O-S, Sulf acidsNIM+N in N-C-N, Im+ ion
NR+N+, Quaternary NN5AX5-ring nitrogen in N-oxide
OMOxide oxygen on Sp3 CFE+2Iron +2 cation
HNR+H-N+FE+3Iron +3 cation
CBAromatic CF-Fluoride anion
NPYDAromatic N, pyridineCL-Chloride anion
NPYLAromatic N, pyrroleBR-Bromide anion
NC=CN-C=C (deloc LP)LI+Lithium cation
CO2MC in CO2- anionNA+Sodium cation
NSPN triple bondedK+Potassium cation
NSO2N, sulfonamidesZN+2Dipositive zinc cation
STHIS in thiopheneCA+2Dipositive calcium cation
NO2Nitro group NCU+1Monopositive copper cation
N=ONitroso group NCU+2Dipositive copper cation
NAZTTerminal N, azideMG+2Dipositive magnesium cation
NSODival. N in S(N)(O) GP



MIF computation through COSMOsar3D

Open3DQSAR allows computing MIFs using the COSMOsar3D program (type=cs3d), which must be in the executable path; if this is not the case, the user shall issue the command

env cs3d=/path/to/cs3d

or alternatively set the O3_CS3D environment variable accordingly.
The user may decide whether to let Open3DQSAR do the whole job (i.e., computing COSMO files via TURBOMOLE and then running COSMOsar3D), or just running COSMOsar3D using pre-computed COSMO files. In the latter case, the file parameter is a wildcard pattern (e.g., /data/COSMO/*.cosmo, or C:\data\ligands\adenosine_????.cosmo) pointing to a series of COSMO files; there must be as many COSMO files as currently loaded objects or an error message will be raised.
Instead, if the user wishes to compute COSMO files as well, the ridft program (part of the TURBOMOLE suite) must be in the executable path; if this is not the case, the user shall issue the command

env qm_engine=/path/to/ridft

or alternatively set the O3_QM_ENGINE environment variable accordingly.
By default, the SVP basis set will be used; alternatively the user may choose the TZVP basis set with the basis_set parameter. TURBOMOLE processes will be spawned in a multi-threaded fashion if n_cpus > 1.
COSMOsar3D descriptors will be computed using the same grid settings as currently defined in Open3DQSAR, with a σ-interval compression coefficient of 6 (see COSMOsar3D documentation and reference [1]). The default value of 6 may be changed through the delsig parameter.



QM ESP/DEN MIF computation

Ab initio quantum mechanics allow to compute electrostatic potential or electron density MIFs. Open3DQSAR can automatically compute such MIFs if appropriate QM software is installed on your system; currently TURBOMOLE, GAUSSIAN, FIREFLY and GAMESS-US are supported. Both FIREFLY and GAMESS-US are available at no cost from the respective websites upon registration. While FIREFLY is available as closed-source binaries for Windows, Linux and Mac OS X (choose the MPICH version), GAMESS-US is available as pre-built binaries for Windows and Mac OS X, and can be easily built from source on both Linux, Solaris and FreeBSD following the instructions. If you use GAMESS-US, please make sure that you have updated to the latest version, since older ones could not compute cube files natively.
No matter which QM engine you will use, the O3_QM_ENGINE environment variable needs to be set to the full path to the executable (e.g., C:\g09\g09.exe on Windows, /usr/local/firefly_71g_linux_mpich_p4/firefly or /usr/local/gamess/gamess.##.x on Linux, /Applications/Firefly/firefly.exe on Mac OS X, etc.); alternatively you may use the env qm_engine keyword. If you choose to use TURBOMOLE, point the O3_QM_ENGINE environment variable (or the qm_engine keyword) to the full path to the dscf executable; e.g. /software/theory/Turbomole/6.3/bin/em64t-unknown-linux-gnu/dscf
Once you have installed on your system a QM software supported by Open3DQSAR, the latter will use it seamlessly, preparing automatically the input files for the computations according to the parameters specified on the calc_field command line and spawning the processes in a multi-threaded fashion if n_cpus > 1.
Alternatively, if you wish to automatically prepare all the input files and then submit them on a batch queueing system such as PBS, or just manually edit some keywords before running the calculations, please refer to the prepare keyword.
Here follows a list of the parameters controlling QM calculations:


MIF computation through Molecular Discovery GRID

Open3DQSAR allows computing MIFs using Molecular Discovery GRID program. The advantage with respect to previous versions is that there is no need to perform the computation externally using the GREATER interface for GRID force-field atom typing, and to import at a later time the MIFs as a GRIDKONT binary file. Open3DQSAR can take care of GRID force-field atom typing automatically, allowing not to break a batch model building workflow.
It is possible to specify the value of the dielectric constant through the diel_const parameter (which defaults to 80.0 as in GREATER), and to choose the upper energy cutoff (which defaults to 5.0 kcal/mol as in GREATER). Any of the GRID probe types can be specified by the probe_type parameter; available probe types are listed below:

Molecular Discovery GRID probe types

C3Methyl CH3 groupF-Fluoride anion
C1=sp2 CH aromatic or vinylCLOrganic chlorine atom
N:#sp N with lone pairCL-Chloride anion
N:=sp2 N with lone pairBROrganic bromine atom
N:sp3 N with lone pairBR-Bromide anion
N-:Anionic tetrazole NIOrganic iodine atom
N1Neutral flat NH eg amideI-Iodide anion
N1+sp3 amine NH cationLI+Lithium cation
N1=sp2 Amine NH cationNA+Sodium cation
N1:sp3 NH with lone pairK+Potassium cation
NH=sp2 NH with lone pairRB+Rubidium cation
N1#sp NH with one hydrogenCS+Caesium cation
N2Neutral flat NH2 eg amideMG+2Magnesium cation
N2+sp3 amine NH2 cationCA+2Calcium cation
N2=sp2 Amine NH2 cationSR+2Strontium cation
N2:sp3 NH2 with lone pairZN+2Zinc cation
N3+sp3 amine NH3 cationCU+2Cupric copper cation
NM3trimethyl-ammonium cationFE+2Ferrous iron cation
O1Alkyl hydroxy OH groupFE+3Ferric iron cation
OHPhenol or carboxy OHBOTHThe Amphipatic Probe
O-sp2 phenolate oxygenDRYThe Hydrophobic Probe
Osp2 carbonyl oxygenCOO-Aliphatic anionic carboxy group
O::sp2 carboxy oxygen atomAR.COO-Aromatic anionic carboxy group
O=O of sulphate/sulphonamideCONH2Aliphatic neutral amide group
OESsp3 ester oxygen atomAR.CONH2Aromatic neutral amide group
OC2Ether or furan oxygenCONHR_CISAliphatic neutral amide group (cis)
OSO of sulphone / sulphoxideCONHR_TRANSAliphatic neutral amide group (trans)
ONOxygen of nitro groupAR.CONHR_CISAromatic neutral amide group (cis)
OH2WaterAR.CONHR_TRANSAromatic neutral amide group (trans)
PO4PO4 phosphate dianionAMIDINEAliphatic cationic amidine group
PO4HPO4H phosphate anionAR.AMIDINEAromatic cationic amidine group
S1Neutral SH groupM-DIAMINEMeta-diamino-benzene
FOrganic fluorine atom


REFERENCES

  1. Klamt, A.; Thormann, M.; Wichmann, K.; Tosco, P. J. Chem. Inf. Model. 2012.   DOI

EXAMPLES

# the following command computes a Van der Waals field using the MMFF94 force-field and the default probe (atom type 1)
calc_field  type=VDW 

# the following commands allow 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
calc_field  type=QM_ELE  theory=DFT  basis_set=6-31G  d_func=1

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

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