24小时热门版块排行榜

返回列表

蓝紫色玻璃心

新虫 (小有名气)

应助: 0 (幼儿园)
金币: 1434.5
帖子: 66
在线: 38.3小时
虫号: 973642
注册: 2010-03-17
专业: 化学计量学与化学信息学

[求助] VMD分析残基RMSD

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

回复此楼