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2Â¥2012-07-01 16:47:22
zhongshun
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3Â¥2012-07-01 21:57:25
jiaoyixiong
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4Â¥2012-07-01 23:45:27
zhongshun
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### Script to immerse ubiquitin in a sphere of water just large enough ### to cover it set molname xia41h mol new ${molname}.psf mol addfile ${molname}.pdb ### Determine the center of mass of the molecule and store the coordinates set cen [measure center [atomselect top all] weight mass] set x1 [lindex $cen 0] set y1 [lindex $cen 1] set z1 [lindex $cen 2] set max 0 ### Determine the distance of the farthest atom from the center of mass foreach atom [[atomselect top all] get index] { set pos [lindex [[atomselect top "index $atom"] get {x y z}] 0] set x2 [lindex $pos 0] set y2 [lindex $pos 1] set z2 [lindex $pos 2] set dist [expr pow(($x2-$x1)*($x2-$x1) + ($y2-$y1)*($y2-$y1) + ($z2-$z1)*($z2-$z1),0.5)] if {$dist > $max} {set max $dist} } mol delete top ### Solvate the molecule in a water box with enough padding (20 A). ### One could alternatively align the molecule such that the vector ### from the center of mass to the farthest atom is aligned with an axis, ### and then use no padding package require solvate solvate ${molname}.psf ${molname}.pdb -t 20 -o del_water resetpsf package require psfgen mol new del_water.psf mol addfile del_water.pdb readpsf del_water.psf coordpdb del_water.pdb ### Determine which water molecules need to be deleted and use a for loop ### to delete them set wat [atomselect top "same residue as {water and ((x-$x1)*(x-$x1) + (y-$y1)*(y-$y1) + (z-$z1)*(z-$z1))<($max*$max)}"] set del [atomselect top "water and not same residue as {water and ((x-$x1)*(x-$x1) + (y-$y1)*(y-$y1) + (z-$z1)*(z-$z1))<($max*$max)}"] set seg [$del get segid] set res [$del get resid] set name [$del get name] for {set i 0} {$i < [llength $seg]} {incr i} { delatom [lindex $seg $i] [lindex $res $i] [lindex $name $i] } writepsf ${molname}_ws.psf writepdb ${molname}_ws.pdb mol delete top mol new ${molname}_ws.psf mol addfile ${molname}_ws.pdb puts "CENTER OF MASS OF SPHERE IS: [measure center [atomselect top all] weight mass]" puts "RADIUS OF SPHERE IS: $max" mol delete top ÎÒ¶Ôsolvate ${molname}.psf ${molname}.pdb -t 20 -o del_waterÕâÒ»ÐÐÃüÁî²»ÊǺܶ®¡£¡£¡£¡£¡£»¹ÓаæÖ÷Ò»°ãʹÓÃʲô¹¤¾ßÀ´½øÐÐÈܼÁ»¯Ñ½£¬×òÌìÊÔÁËÏÂpackmol£¬µ«Ö»Êǵõ½ÁËpdbÎļþ£¬²»ÖªµÀpsfÎļþÔõôµÃµ½£¿ |
5Â¥2012-07-02 09:43:13
jiaoyixiong
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zhongshun: ½ð±Ò+20, ¡ïÓаïÖú 2012-07-02 17:24:03
zh1987hs: ½ð±Ò+4, лл 2012-07-02 18:34:30
zhongshun: ½ð±Ò+20, ¡ïÓаïÖú 2012-07-02 17:24:03
zh1987hs: ½ð±Ò+4, лл 2012-07-02 18:34:30
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6Â¥2012-07-02 10:35:15
zhongshun
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7Â¥2012-07-02 18:14:16
zmz148002989
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8Â¥2012-07-18 20:52:46
zhongshun
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9Â¥2012-07-18 23:18:32
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