#vmd默认使用stride计算蛋白二级结构，这里给出vmd提出dssp计算的二级结构并输出到一个文件中用于作图，文件输出格式类似Amber的输出格式，其中X代表不规则卷曲或者loop，将以下代码保存为test.tcl可以直接在终端下运行以下命令：

#vmd test.psf test.dcd -dispdev text -e test.tcl

#如果是amber的拓扑文件和轨迹则为

#vmd -parm7 test.prmtop -crdbox test.mdcrd -dispdev text -e test.tcl

#输出的文件为sec4traj.txt

1 # dealing with data in DSSP file 


    2 proc myproc1 {a b framei} {


    3 # creat a empty list


    4   set newsecdata [list]


    5   set linenumber 0


    6   foreach a $b {


    7     incr linenumber


    8     if {[string equal [string index $a 2] #]} {


    9       puts "The line number is $linenumber"


   10       set secdata [lrange $b $linenumber end]


   11 #     puts $secdata 


   12       foreach secinfo $secdata {


   13         set sectype [string index $secinfo 16]


   14         if {[string is space $sectype]} then {


   15           lappend newsecdata X


   16         } else {


   17           lappend newsecdata $sectype


   18         }


   19       }


   20     }


   21   }


   22   set mynewsecdata [join $newsecdata \t]


   23   set secdataframe [linsert $mynewsecdata 0 $framei]


   24   puts $secdataframe


   25   set sectraj [open sec4traj.txt a]


   26   puts $sectraj $secdataframe


   27   close $sectraj


   28 } 


   29 


   30 # generate each frame pdb file and analyze secondary structure with dssp


   31 set n [molinfo top get numframes]


   32 puts "===Analysis number of frames: $n"


   33 set myprotein [atomselect top protein]


   34 #write resids


   35 set myresids [lsort -integer -unique [$myprotein get resid]]


   36 


   37 set sectraj [open sec4traj.txt w]


   38 puts $sectraj $myresids


   39 close $sectraj


   40 


   41 #analysis of frames


   42 for { set i 0 } { $i < $n } { incr i } {  


   43   $myprotein frame $i  


   44   $myprotein update  


   45   $myprotein writepdb myptrotein_$i.pdb


   46   exec mkdssp -i myptrotein_$i.pdb -o myptrotein_$i.dssp


   47 注意，这里的mkdssp是你的dssp程序的命令，有的人安装了是dssp，我这里是mkdssp，只要换成你安装的名字即可

   48   set dsspfile [open myptrotein_$i.dssp r]


   49   set dsspline [read $dsspfile ]


   50   set dsspdata [split $dsspline \n]


   51   close $dsspfile


   52   myproc1 splitdata $dsspdata $i


   53   


   54   


   55   file delete myptrotein_$i.pdb


   56   file delete myptrotein_$i.dssp


   57 }