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【求助】水總?cè)ゲ坏�，�?qǐng)指點(diǎn)（已解決，謝謝各位幫助） 已有2人參與
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生成進(jìn)通道中含水分子的pdb文件： 1. 通過(guò)vmd先找到通道中的水分子，獲取它們的編號(hào) 2. 然后生成這些水分子的pdb文件（例子）： mol load pdb 1YMG.pdb set model [atomselect top "water and (resid 411 or resid 415 or resid 455 or resid 426 or resid 407 or resid 426)"] $model writepdb wat.pdb exit 3. 生成蛋白的pdb文件： mol load pdb 1YMG.pdb set model [atomselect top protein] $model writepdb 1ymg.pdb exit 4. 合并wat.pdb 與1ymg.pdb 這一步不用寫(xiě)腳本，直接把wat.pdb的內(nèi)容（即去頭去尾）拷貝到1ymg.pdb的END前即可。 5. over。 構(gòu)建四聚體(buildtetra.tcl): mol load pdb 1ymg.pdb set all [atomselect top all] $all set segname A $all writepdb AQP1-A.pdb $all delete set sel [atomselect top all] $sel set segname B $sel move {{-1.0 0.0 0.0 0.0} {0.0 -1.0 0.0 110.531} {0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}} $sel writepdb AQP1-B.pdb $sel delete mol delete top mol load pdb 1ymg.pdb set sel [atomselect top all] $sel set segname C $sel move {{0.0 -1.0 0.0 55.2655} {1.0 0.0 0.0 55.2655} {0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}} $sel writepdb AQP1-C.pdb $sel delete mol delete top mol load pdb 1ymg.pdb set sel [atomselect top all] $sel set segname D $sel move {{0.0 1.0 0.0 -55.2655} {-1.0 0.0 0.0 55.2655} {0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}} $sel writepdb AQP1-D.pdb $sel delete cat AQP1-A.pdb AQP1-B.pdb AQP1-C.pdb AQP1-D.pdb > AQP1.pdb 然后打開(kāi)AQP1.pdb,搜索END,把中間的三個(gè)END及相應(yīng)的雜項(xiàng)去掉，保存為AQP1-ALL.pdb。此時(shí)就生成了四聚體pdb文件。 進(jìn)行psf生成前的文件準(zhǔn)備(prepfiles.tcl)： mol load pdb AQP1-ALL.pdb foreach S {A B C D} { set seg [atomselect top "segname $S and chain A"] $seg writepdb seg$S.pdb $seg delete } foreach S {A B C D} { set wat [atomselect top "segname $S and resname HOH and within 100 of chain A"] $wat writepdb crystwat$S.pdb $wat delete } exit 產(chǎn)生psf文件（build.psf）: package require psfgen topology ../top_all27_prot_lipid.rtf pdbalias residues HIS HSE pdbalias atom ILE CD1 CD pdbalias atom HOH O OH2 pdbalias resid HOH TIP3 foreach S {A B C D} { segment $S { pdb seg$S.pdb } coordpdb seg$S.pdb $S regenerate angles dihedrals segment WC$S { auto none pdb crystwat$S.pdb } coordpdb crystwat$S.pdb WC$S } guesscoord writepdb aqp1.pdb writepdb aqp1.psf exit solvating過(guò)程： 先加載上一步產(chǎn)生的psf pdb文件，然后 set sel [atomselect top all] measure minmax $sel solvate -t 3 -minmax {上一步得到的值} -o solaqp1 然后寫(xiě)make_solv.tcl腳本： set sol_infile solaqp1.pdb set aqp1_inbase aqp1 set outbase aqp1_solv_raw package require psfgen resetpsf readpsf solaqp1.psf coordpdb solaqp1.pdb readpsf ${aqp1_inbase}.psf coordpdb ${aqp1_inbase}.pdb writepdb ${outbase}.pdb writepsf ${outbase}.psf exit 估測(cè)所需膜尺寸： 先把我加水并運(yùn)行過(guò)make_solv.tcl所產(chǎn)生的psf pdb加載，然后再 set all [atomselect top all] measure $all minmax [][] 然后x2-x1 y2-y1 將蛋白的重心和水盒子的重心重合： mol load psf aqp1_solv_raw.psf pdb aqp1_solv_raw.pdb set all [atomselect top all] $all moveby [vecinvert [measure center $all]] display resetview 然后估測(cè)刪除水的值： 將膜的psf pdb加載，然后 set sel [atomselect top lipid] measure minmax $sel 選擇z2 的整數(shù)值:25 然后： set solv [atomselect top "segname SOLV"] $solv set beta 1 set seltext "segname SOLV and same residue as ((z < -25) or (z > 25))" set sel [atomselect top $seltext] $sel set beta 0 set badwater [atomselect top "name OH2 and beta > 0"] set seglist [$badwater get segid] set reslist [$badwater get resid] mol delete all package require psfgen resetpsf topology ../top_all27_prot_lipid.rtf readpsf aqp1_solv_raw.psf coorpdb aqp1_solv_raw.pdb foreach segid $seglist resid $reslist { delatom $segid $resid } writepdb aqp1_solv.pdb writepsf aqp1_solv.psf 出現(xiàn)的問(wèn)題： 選擇需要去掉的水分子，根本去不掉。我也知道一部分原因：因?yàn)槲以趍ake_solv.tcl腳本中把segment SOLV那一段給刪除了，應(yīng)該還有其他的原因。我現(xiàn)在把有水盒子的pdb及make_solv.tcl所產(chǎn)生的pdb傳上來(lái)，大家?guī)兔Ψ治鲆幌隆Ｏ戎x謝了 http://u.115.com/?ct=index&a ... d=1&cid=2023017 這個(gè)鏈接的用戶名：tonme 密碼：002725 [ Last edited by nufang19a on 2011-2-28 at 11:47 ] |
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wally8962
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zh1987hs(金幣+4): 謝謝！ 2011-02-26 22:47:39
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zh1987hs(金幣+4): 謝謝！ 2011-02-26 22:47:39
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"cat AQP1-A.pdb AQP1-B.pdb AQP1-C.pdb AQP1-D.pdb > AQP1.pdb 然后打開(kāi)AQP1.pdb,搜索END,把中間的三個(gè)END及相應(yīng)的雜項(xiàng)去掉，保存為AQP1-ALL.pdb。此時(shí)就生成了四聚體pdb文件。" 這個(gè)步驟是多余的，后面根本用不到這個(gè)四聚體，直接用前面的單體就行了。 你想去掉孔道中的水分子？那晶體中的水分子可以一個(gè)都不用。 后面孔道中的水分子很可能是你solvate時(shí)加進(jìn)去的�？梢杂�-b調(diào)整水分子距蛋白的距離來(lái)控制加入的水分子。 更簡(jiǎn)單的，在vmd中，按數(shù)字鍵“6”，鼠標(biāo)變成拖弋模式，直接把水分子拖出來(lái)，再保存pdb [ Last edited by wally8962 on 2011-2-26 at 18:36 ] |
2樓2011-02-26 18:35:41
3樓2011-02-26 22:51:05
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難道跟NAMD tutorial最后面的這一段有關(guān)： ### Solvate the molecule in a water box with enough padding (15 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 ${molname}.pdb -t 15 -o del_water resetpsf package require psfgen mol new del_water.psf mol addfile del_water.pdb readpsf del_water.psf coordpdb del_water.pdb ### Determine which water molecules need to be deleted and use a for loop ### to delete them set wat [atomselect top "same residue as {water and ((x-$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 |
4樓2011-02-27 00:24:45
5樓2011-02-27 15:35:56
6樓2011-02-27 16:07:41
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我先估測(cè)了膜的尺寸： 先把我加水并運(yùn)行過(guò)make_solv.tcl所產(chǎn)生的psf pdb加載，然后再 set all [atomselect top all] measure minmax $all [][] 然后x2-x1 y2-y1，將膜建好 再然后我有估測(cè)了需要?jiǎng)h除的水分子： 將膜的psf pdb加載，然后 set sel [atomselect top lipid] measure minmax $sel 選擇z2 的整數(shù)值:25 再然后： set solv [atomselect top "segname SOLV or segname WT1"] $solv set beta 1 set seltext "segname SOLV and same residue as ((z < -25) or (z > 25))" set sel [atomselect top $seltext] $sel set beta 0 set badwater [atomselect top "name OH2 and beta > 0"] set seglist [$badwater get segid] set reslist [$badwater get resid] mol delete all package require psfgen resetpsf topology ../top_all27_prot_lipid.rtf readpsf aqp1_solv_raw.psf coorpdb aqp1_solv_raw.pdb foreach segid $seglist resid $reslist { delatom $segid $resid } writepdb aqp1_solv.pdb writepsf aqp1_solv.psf 那么刪除水分子的過(guò)程，難道不對(duì)？？ [ Last edited by nufang19a on 2011-2-27 at 16:28 ] |
7樓2011-02-27 16:16:41
8樓2011-02-27 19:05:32
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ghcacj(金幣+10): LZ一貫喜歡自彈自唱，呵呵，謝謝分享解決方法。 2011-02-28 13:52:38
ghcacj(金幣+10): LZ一貫喜歡自彈自唱，呵呵，謝謝分享解決方法。 2011-02-28 13:52:38
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解決了，另外水的厚度不夠，在z軸方向有加了5A的水分子。 解決方法（還要保留孔道中的結(jié)晶水）： 刪除水(remove_wat.tcl)： mol load psf aqp1_solv_raw.psf pdb aqp1_solv_raw.pdb set all [atomselect top all] $all moveby [vecinvert [measure center $all]] display resetview set solv [atomselect top water] $solv set beta 1 set seltext "water and ((z<-25) or (z>25)) or (segname WCA) or (segname WCB) or (segname WCC) or (segname WCD)" set sel [atomselect top $seltext] $sel set beta 0 set badwater [atomselect top "name OH2 and beta >0"] set seglist [$badwater get segid] set reslist [$badwater get resid] mol delete all package require psfgen resetpsf topology ../top_all27_prot_lipid.rtf readpsf aqp1_solv_raw.psf coordpdb aqp1_solv_raw.pdb foreach segid $seglist resid $reslist { delatom $segid $resid } writepdb aqp1_solv.pdb writepsf aqp1_solv.psf exit |
9樓2011-02-28 11:46:37
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