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Organizei mais essa seção para compartilhar informações sobre software IGMPlot.
O IGMPlot é um software de Química Teórica para o cálculo de interações inter e intramoleculares.
Fiz o downloado do pacote IGMPlot-2.6.9b.tbz2, descompactei e fiz a compilação do programa IGMPlot sem problemas com o comando make no diretório “/home/markos/Química/Computacional/IGMPLOT-2.6.9b/source”.
Depois da compilação rodei o script de teste com o comando python3 IGMPLOT_test_samples.py ../IGMPLOT ../../samples seguindo as orientações do documento ...IGMPLOT-2.6.9b/source/scripts/README.
O teste foi rápido até o exemplo 9, e depois ficou muuuiito lento ocupando toda a carga do processador.
E a saída foi:
python3 IGMPLOT_test_samples.py ../IGMPLOT ../../samples
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/01_example/test01 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/01_example/test02 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/02_example/test03 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test04 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test05 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test06 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test07 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test08 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test09 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/03_example/test10 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/04_example/test11 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/04_example/test12 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/05_example/test13 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/06_example/test14 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/07_example/test15 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/08_example/test16 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/08_example/test17 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/09_example/test18 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/10_example/test19 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/11_example/test20 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/12_example/test21 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/13_example/test22 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/14_example/test23 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/15_example/test24 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/16_example/test25 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/17_example/test26 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/17_example/test27 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/17_example/test28 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/17_example/test29 OK
/home/markos/Química/Computacional/IGMPLOT-2.6.9b/samples/18_example/test30 OK
Segundo o manual: “The IGM-dg approach is based on the possibility to define two fragments whose interaction is studied (even though intramolecular interactions will be also delivered).”.
Para rodar o programa é necessário passar dois arquivos como argumentos de entrada: o arquivo de parâmetros de entrada “param.igm”, e um arquivo com dados da(s) moléculas que podem ser no modo (QM - Mecânica Quântica) ou Promolecular.
Na página 13 do manual podemos ler:
Two kinds of files are needed:
-the parameter input file param.igm
- either:
QM mode: one single file to specify both the geometry and the wave function (.wfn or .wfx,)
Promolecular mode:
§ Two .xyz files to specify the geometry of the two fragments
§ One .xyz file : the system will be considered as a whole (dg inter =0)
Mas o que é o arquivo “wfn” e “wfx”? (Fonte: http://aim.tkgristmill.com/wfxformat.html)
Format specification for AIM Extended Wavefunction Files (.wfx files) Version 1.0.4c "AIM Extended Wavefunction Files" (.wfx files) are newer versions of "AIM Traditional Wavefunction Files" (.wfn files). The original purpose of .wfx files (relative to .wfn files) was to present essentially the same data as in .wfn files, but in a cleaner way that allows easy, free-format reading and writing of wavefunction data of unlimited size, range and precision and that allows for the possible addition of more kinds of data in a non-disruptive way. In the current specification, .wfx files (like .wfn files) are limited to first-order density matrices (total or alpha and beta) expressed in an MO basis.
Input -from a wave function file: two input files are needed: one wfn or wfx file describing the wave function (and the geometry) and in addition, a “.igm” parameter file containing the keywords. The definition of the two fragments to be studied can be set is set through the keyword FRAG1, FRAG2 or CUBEFRAG (see below). - with promolecular ED: in the standard case three input files are needed: two xyz file describing the cartesian coordinates of the two interacting partners; in addition, a “.igm” file containing the keywords is needed. It is also possible to use the program to study non-covalent interactions within one single molecule: only one single .xyz input file is required in that case instead of two. The electron density (ED) is then calculated directly by IGMPlot using the promolecular approximation.
param.igm constrained format:
The first line must contain the number n of files describing the molecular system. Currently, n is an integer in the range [1-2]. n=1 if you intend to use a wave function file (wfn or wfx). n=1 or n=2 if you intend to use promolecular density (xyz mode). According to the filename extension supplied immediately after (.xyz or .wfn or .wfx) IGMPlot will appropriately proceed with a promolecular or wave function calculation. The second line must contain the name of the first .xyz coordinate file (or of the wfn file or wfx file). If 2 files have to be read (promolecular mode), the second and third lines must contain the two names of the first and second .xyz files.
Exemplo:
2
ligand.xyz
protein.xyz
Definição do termo “promolecular”:
Definition of the Promolecule
Fonte: https://pubs.acs.org/doi/pdf/10.1021/j100401a010 Chemical properties from the promolecule M. A. Spackman and E. N. Maslen J. Phys. Chem. 1986, 90, 10, 2020-2027
The term promolecule, originally used by Hirshfeld and Rzotkiewicz,2b refers to a reference electron density model prior to molecule formation.
Rodando o programa na pasta IGMPLOT-2.6.9b/samples/01_example/test01 com o comando ../../../source/IGMPLOT param.igm.
Tivemos a saída:
Sun Sep 25 16:13:59 2022
Reading input data ...
---------------------------------------------------------------------
* *
* I G M P L O T *
* Rev. 2.6.9b - June 2021 *
* Identifying and Characterizing Interactions *
* in Molecules *
* *
* PROGRAM AUTHORS *
* . Johanna Klein *
* . Pluot Emmanuel *
* . Rubez Gaetan *
* . Boisson Jean-Charles *
* . Henon Eric *
* *
* --------------- Champagne-Ardenne University ----------------- *
* *
* CONTRIBUTORS *
* . H. Khartabil *
* . C. Lefebvre *
* . M. Ponce-Vargas *
* . J. Contreras-Garcia *
* *
* Please cite *
* Phys Chem Chem Phys 2017, 19(27), 17928-17936 *
* Chem. Phys. Chem. 2018, 19 , 724-735 *
* *
* ---------------------------------------------------------------- *
* Density type : PROMOLECULAR *
* *
* IGM Model : dg, dgInter, dgIntra, dgAt descriptors *
* Cubic grid *
* Atomic contributions calculated *
* *
* NbFiles : 2, fragmentation scheme *
* *
* MoleculeFile [0] : frag1.xyz / 3 atoms *
* MoleculeFile [1] : frag2.xyz / 3 atoms *
* *
* Number of thread(s) : 8 *
* *
* gridBox Definition : LIGAND *
* gridBox MIN (bohr) : -9.32 -5.89 -5.67 *
* gridBox MAX (bohr) : 4.54 7.11 5.67 *
* Increments (bohr) : 0.19 0.19 0.19 *
* NbSteps : 74 69 61 *
* *
* INTERMOLECULAR (NCI) : 100.00 % *
* .dat rho range (r1) : [-3.00e-01: 3.00e-01] -> nci+igm dat *
* .dat rdg range (r2) : [ 0.00e+00: 1.00e+01] -> nci dat *
* .cube rho range (r3) : [-2.50e+00: 2.50e+00] -> RDG cube *
* .cube rho range (r5) : [-1.20e+00: 1.20e+00] -> dgIntra cube *
* .cube rho range (r6) : [-3.00e-01: 3.00e-01] -> dgInter cube *
* RDG isoval. (r4) : 3.00e-01 -> vmd RDG *
* ED color scale (r7) : 3.00e-01 -> vmd dgIntra *
* ED color scale (r8) : 8.00e-02 -> vmd dgInter *
* *
* OUTPUT type : 5 *
* File 1 : out-nci.dat *
* File 2 : out-igm.dat *
* File 3 : out-dens.cube *
* File 4 : out-RDG.cube *
* File 5 : out-dgInter.cube *
* File 6 : out-dgIntra.cube *
* File 7 : nci.vmd *
* File 8 : igm.vmd *
* File 9 : atContr.vmd *
* File 10 : out-complex.xyz *
* File 11 : out-percent.dat *
* *
* ########################## I N T E R ########################### *
* ---------------------------------------------------------------- *
* T Y P E o f I N T E R A C T I O N *
* *
* MAXIMUM of the dg peak(s) = 5.4941e-02 a.u. (attractive part) *
* dg SCALE: *
* | *
* | *
* v *
* |___________|________________|______________________________| *
* 0 0.1 0.6 2.5 *
* < non-cov > < metal coord > *
* < ................... covalent ............. > *
* *
* ---------------------------------------------------------------- *
* Q U A N T I F I C A T I O N o f I N T E R A C T I O N *
* between FRAGMENT(S) *
* *
* . Non-zero values of dg[Inter] exclusively corresponds to *
* molecular interaction situations *
* => greatly facilitates integration *
* *
* . The integration scheme has been developed to relate the sum *
* of dgInter to the strength of interaction between fragments *
* ONLY DEDICATED TO NON-COVALENT INTERACIONS *
* *
* Grid Integration score: *
* *
* [1] sum dg[Inter] x dv = 2.81e-01 a.u. *
* [2] sum_v[IGM] -dg[Inter] x dv = -9.20e-02 a.u. *
* *
* [3] Inter. Energy crude Estimate = -5.50e+00 kcal/mol *
* *
* *
* Integration region: *
* [1] : Entire grid *
* [2] : Space where (gradRhoIGMInter / gradRho) > 1.2 and L2 < 0 *
* to focus on attractive dg[Inter] peaks only *
* [3] : Estimated from [2] (see doc for appropriate use) *
* *
* ########################## I N T R A ########################### *
* ---------------------------------------------------------------- *
* Q U A N T I F I C A T I O N o f I N T E R A C T I O N *
* within FRAGMENT(S) *
* *
* Grid Integration score: *
* *
* [1] sum dg[Intra] x dv = 1.6064306077e+00 a.u. *
* *
* [2] sum_v -dg[Intra_weak] x dv = 0.0000000000e+00 a.u. *
* *
* Integration region: *
* [1] Entire grid *
* [2] -0.09 < ED < 0.00, gradRhoIGM/gradRho > 1.4 *
* *
* Note: Integration [1] may contain strong and weak interactions; *
* Promolecular ED can only address the non-covalent domain *
---------------------------------------------------------------------
CPU time : 0s
Writing files ...
Wall-clock time : 1s
Sun Sep 25 16:14:00 2022
Done
Para instalar o VMD (Programa de visualização) baixei o arquivo vmd-1.9.4a57.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz na página: https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD.
Descompactei com o comando tar -xzvf vmd-1.9.4a57.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
Abri o manual de instalação (ig.pdf) no diretório vmd-1.9.4a57/doc
E segui as etapas do manual de instalação:
To install the pre-compiled Unix version of VMD, then only three steps remain to be done after you uncompress and untar the distribution.
Edit the configure script. If necessary, change the following values:
$install_bin_dir
This is the location of the startup script “vmd”. It should be located in the path of users interested in running VMD.
$install_library_dir
This is the location of all other VMD files. This includes the binary and helper scripts. It should not be in the path.
Next generate the Makefile based on these configuration variables. This is done by running ./configure .
After configuration is complete, cd to the src directory and type make install, as root.
Depois disso é só executar o VMD digitando vmd no terminal.
Para visualizar os modelos moleculares basta abrir os arquivos .vmd que estão na pasta IGMPLOT-2.6.9b/samples.
IGMPLOT-2.6.9b/samples$ ls
01_example 05_example 09_example 13_example 17_example README_timings
02_example 06_example 10_example 14_example 18_example
03_example 07_example 11_example 15_example logs
04_example 08_example 12_example 16_example README