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[求助]
VMD分析残基RMSD
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看网上说用VMD自带的rmsd-fullthrottle.tcl文件就可以对指定残基计算RMSD，但是这个文件不是很明白（对程序一点都不明白 ），想问一下有没有用这个程序计算RMSD的？我对这个文件里面应该修改什么？或者能不能给个具体步骤？一点头绪都没有！# This script contains a procedure called rmsd_residue_over_time that calculates the average RMSD for each residue in a selection over all frames in a trajectory. The procedure is called as: # rmsd_residue_over_time mol sel_resid #where mol is the molecule in VMD and sel_resid is a list of the residue numbers in that selection. #You can use the procedure for any residue or list of residues. Here, as an example, we will make a selection for all residues in the protein. Note that this will take a long time to calculate: set sel_resid [[atomselect top "protein and alpha"] get resid] #The procedure is presented below. It also sets the B value to the value calculated, so you can color the protein by RMSD. The call for the procedure is at the end of the file. proc rmsd_residue_over_time {{mol top} res} { # use frame 0 for the reference set reference [atomselect 1 "protein" frame 0] # the frame being compared set compare [atomselect $mol "protein"] #make a selection with all atoms set all [atomselect top all] #get the number of frames set num_steps [molinfo $mol get numframes] foreach r $res { set rmsd($r) 0 } #loop over all frames in the trajectory for {set frame 1} {$frame < $num_steps} {incr frame} { puts "Calculating rmsd for frame $frame ..." # get the correct frame $compare frame $frame # compute the transformation set trans_mat [measure fit $compare $reference] # do the alignment $all move $trans_mat # compute the RMSD #loop through all residues foreach r $res { set ref [atomselect $mol "chain U and resid $r and noh" frame 0] set comp [atomselect $mol "chain U and resid $r and noh" frame $frame] set rmsd($r) [expr $rmsd($r) + [measure rmsd $comp $ref]] $comp delete $ref delete } } set ave 0 foreach r $res { set rmsd($r) [expr $rmsd($r)/$num_steps] # print the RMSD puts "RMSD of residue $r is $rmsd($r)" set res_b [atomselect $mol "resid $r"] $res_b set beta $rmsd($r) $res_b delete set ave [expr $ave + $rmsd($r)] } set ave [expr $ave/[llength $res]] puts " Average rmsd per residue: $ave" } #Call the procedure rmsd_residue_over_time top $sel_resid |
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