VMD scripts

# mostrar o complexo (resid 1) e as aguas a 3 angstrons do cobre (index 3)
(water or resid 1) and same residue as (within 3 of index 3)
(water or nucleic) and within 3.5 of name Cu
water and same residue as (within 2.5 of resid 1)
water within 2.5 of resid 1
resid 2 3 and within 20 of index 13
name OW and (within 2 of backbone)
resname CIE DA DT DC DG and (within 4 of resname CIE)
resname 'Na+'
all and not resname "Cl-"

# coloque 'update selection' na guia trajectory
nucleic and (within 7 of resname CIE)
# neste caso vai selecionar so os átomos do nucleic que estao perto do serial 4
nucleic and (within 3 of resname CIE and serial 4)

#Selecionar apenas o restante das moleculas sem incluir o CIE
not resname CIE and within 5 of resname CIE

index 10 11 12
index 10 to 12

resname QUA pro
residue cys ala
resid 1 2 3

type H HO
element H C N O (?)

protein not hydrogen

vmd –parm7 acetone_solv.top –rst7 acetone_solv.rst
vmd –parm7 acetone_solv.top –crdbox “outputfile”.crd
mol addfile equil-press/equil-$i.crd type crdbox waitfor all

# diferença entre resid e residue

residue 0 to 342 # mostra os resíduos de um único domínio
resid 1 to 343 # mostra os resíduos dos vários domínios enumerdos de 1 até n. Normalmente as moléculas de água e os aminoácidos iniciam por 1, desta forma quando o selecionamos os dois aparecem na tela.

#Habilitar o log para verificar a ação equivalente da linha de comando
# no terminal digite:
log nome.log

log off

#Load script files
vmd -e load.tcl
vmd -e vmd.vmd

cat load.tcl
#LOAD FILES
set mol [mol new cie_solv.top type parm7 waitfor all]
for {set i 3} {$i <= 7} {incr i} {
    mol addfile cie_solv_md$i.mdcrd type netcdf waitfor all
}

#gravar arquivo pqr

vmd -dispdev text
set mol [mol new prot_solv.top type parm7 waitfor all]
mol addfile reimaged14.rst.1 type rst7
animate write pqr test.pqr
#animate write pqr {/home/marcos/Desktop/rst/aaaaaaa.pqr} beg 0 end 0 skip 1 0

#gravar trajetória e pdb de frames e seleção específica (não funciona porque as H2O se afastam)
vmd -dispdev text
set mol [mol new cie_solv.top type parm7 waitfor all]
mol addfile output.cdf type netcdf first 0 last 2000 step 1 waitfor all
set sel [atomselect top "all and same residue as (within 5 of resname CIE)"]
animate write dcd com_traj.dcd beg 1 end 2000 sel $sel
animate write pdb com_traj.pdb beg 1 end 1 sel $sel

# adicionar label pela linha de comando
label add Atoms 0/6323
label addspring 0 4296 4299 1


vmd > label
label add [Atoms|Bonds|Angles|Dihedrals] {atoms as /}
label addspring
label list              -- return label categories
label list   -- return id's of labels in given category
label [show|hide|delete] [index] -- 
Control specific label or all labels in category
label graph -- Return a list of values for the given label
for all animation frames
label textsize []
label textthickness []

# convenções no VMD
resid no VMD pode ser mais de um tipo de residuo, por ex:
resid 1 quer dizer os residuos CIE 1 e também a primeira molécula de água: SOLV 1
Assim pra salvar mais de um composto pode ser interessante utilizar: "resname CIE or resid 234 765", assim salvará apenas 3 resíduos


From:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node192.html

VMD Command-Line Options

When started, the following command-line options may be given to VMD. Note that if a command-line option does not start with a dash (-), and is not part of another option, it is assumed to be a PDB filename. Thus, the Unix command

        vmd molecule.pdb

will start VMD and load a molecule from the file molecule.pdb. On the Windows platform, one must preface the VMD invocation with the Windows start command

        start vmd molecule.pdb

• -m : Load all subsequent files into separate molecules. The -f and -m options may be specified multiple times on the command line in order to load multiple molecule containing one or more files.

• -h | -? : Print a summary a command-line options to the console.
• -e filename : After initialization, execute the text commands in filename, and then resume normal operation.
• -psf filename : Load the specified molecule (in PSF format) at startup. The PSF file only contains the molecular structure; a PDB or DCD file must also be specified when this option is used.
• -pdb filename : Load the specified molecule (in PDB format) at startup.
• -dcd filename : Load the specified trajectory file (in binary DCD format) at startup. The DCD file only contains atomic coordinates; a PDB or PSF file must also be specified when this option is used.
• - filename : Load the specified file using the given filetype.
• -f : Load all subsequent files into the same molecule. This is the default. A new molecule is created for each invocation of -f; thus, vmd -f 1.pdb 2.pdb -f 3.pdbloads 1.pdb and 2.pdb into the same molecule and 3.pdb into a different molecule.
• 
  
• -dispdev < win | text | cave | caveforms | none > : Specify the type of graphical display to use. The possible display devices include:
  • win: a standard graphics display window.
  • text: do not provide any graphics display window.
  • cave: use the CAVE virtual environment for display, forms are disabled.
  • caveforms: use the CAVE virtual environment for display and with forms enabled. This is useful with -display machine:0 for remote display of the forms when the CAVE uses the local screen.
  • none: same as text.
  It is possible to use VMD as a filter to convert coordinate files into rendered images, by using the -dispdev text and -e options.
• -dist z : Specify the distance to the VMD image plane.
• -height y : Specify the height of the VMD image plane.
• -pos x y : Specify the position for the graphics display window. The position (x,y) is the number of pixels from the lower-left corner of the display to the lower-left corner of the graphics window.
• -size x y : Specify the size for the graphics display window, in pixels.
• -nt : Do not display the VMD title at startup.
• -startup filename : Use filename as the VMD startup command script, instead of the default .vmdrc or vmd.rc file.
• -debug [level : Turn on output of debugging messages, and optionally set the current debug level (1=few messages ... 5=many verbose messages). Note this is only useful if VMD has been compiled with debugging option included.