VMD统计一帧中聚合物的二面角求助

ZZU_SCU

聚合物是该结构，我要统计所有酰胺键的二面角C2-N2-C4-C2。所有红色的碳原子均是C2，酰胺键的碳是C4，酰胺键的氮是N2。为了避免选择错误的C2原子，写的Tcl文件如下。输出结果都是* * * 2的二面角，感觉不对。请大家指导迷津 Dihedral.dat (84 KB, 下载次数 Times of downloads: 7)

2023-2-22 19:51 上传 Uploaded

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   150 (9.09 MB, 下载次数 Times of downloads: 9)

2023-2-22 20:04 上传 Uploaded

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请添加.xyz后缀，接着用VMD打开

1. set a [atomselect top "name N2"]
   
2. set myfile [open Dihedral.dat w]
   
3. set l1 [$a get index]
   
4. foreach ind $l1 {
   
5. set b [atomselect top "name C2 and withinbonds 1 of index $ind"]
   
6. set d [atomselect top "name C4 and withinbonds 2 of index $ind"]
   
7. set c [atomselect top "name C2 and withinbonds 1 of index $d"]
   
8. 
   
9. if {[$b num]==1 && [$c num]==1 && [$d num]==1} {
   
10. set l2 [$b get index]
    
11. set l3 [$c get index]
    
12. set l4 [$d get index]
    
13. set tmp [list $l2 $ind $l4 $l3]
    
14. set result [measure dihed $tmp]
    
15. puts $myfile "$l2 $ind $l4 $l3 $result"
    
16. }
    
17. }
    
18. puts "All Done!"

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