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wuhanhgf2002金虫 (正式写手)
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[交流]
【求助】关于氢键
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请问有没有查询mol2结构中氢键供体和受体数目的软件？最好是linux下的。谢谢 [ Last edited by zdhlover on 2009-11-25 at 13:09 ] |
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wuhanhgf2002
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2楼2009-03-10 09:23:40
superdirac
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3楼2009-03-10 17:14:32
bay__gulf
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xuefei06(金币+6,VIP+0):thanks！ 3-10 23:41
xuefei06(金币+6,VIP+0):thanks！ 3-10 23:41
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vmd 提供了计算HB的接口，但具体用法需要自己写脚本。 下面是一个计算水中每个分子同周围形成氢键的数目。最关键的是 measure hbonds $dist $ang 这一行，但全文我还没有看明白。 set all [atomselect top all] # determine the dimensions of the water box set mes [measure minmax $all] set xmin [lindex [lindex $mes 0] 0] set ymin [lindex [lindex $mes 0] 1] set zmin [lindex [lindex $mes 0] 2] set xmax [lindex [lindex $mes 1] 0] set ymax [lindex [lindex $mes 1] 1] set zmax [lindex [lindex $mes 1] 2] set O [atomselect top "name OH2"] # set the number of atoms for which you want to count H-bonds set atomcount 300.0 set totalbondnum 0 for {set i 1} {$i <= $atomcount} {incr i} { # pick a random water molecule (oxygen atom) and record its position set rand [expr int(rand()*[expr [$O num] - 1])] set oatom [atomselect top "index [lindex [$O get index] $rand]"] set xpos [lindex [lindex [$oatom get {x y z}] 0] 0] set ypos [lindex [lindex [$oatom get {x y z}] 0] 1] set zpos [lindex [lindex [$oatom get {x y z}] 0] 2] set buffer 3 # the selected atom should be away from the surface (by if {$xpos < [expr $xmin+$buffer] || $xpos > [expr $xmax-$buffer] || $ypos < [expr $ymin+$buffer] || $ypos > [expr $ymax-$buffer] || $zpos < [expr $zmin+$buffer] || $zpos > [expr $zmax-$buffer]} then { set i [expr $i-1] } else { # set the distance of a H-bond to 3.0 Angstroms and the angle to 30 degrees (default values) set dist 3.0 set ang 30.0 set temp1 [atomselect top "same residue as index [$oatom get index]"] set temp2 [atomselect top "same residue as exwithin 10 of index [$temp1 get index]"] # count the number of H-bonds for th molecule set count1 [llength [lindex [measure hbonds $dist $ang $temp1 $temp2] 0]] set count2 [llength [lindex [measure hbonds $dist $ang $temp2 $temp1] 0]] # and add it to the total so far set totalbondnum [expr $totalbondnum+$count1 + $count2] } } puts "Each water molecule makes [expr double($totalbondnum/$atomcount)] hydrogen bonds on average with its neighbors." |
4楼2009-03-10 17:58:13
5楼2009-03-11 09:36:38
