[交流] 【在线答疑】关于NAMD/VMD已有27人参与

Originally posted by jianchaoyv at 2009-11-15 13:28:
>Main< (vmd) 3 % source ubq.pgn
couldn't read file "ubq.pgn": no such file or directory

请问怎样解决这个问题，初学VMD请高手指教！！

Originally posted by jianchaoyv at 2009-11-16 16:49:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: can't read "coorList(577)": no such element in array
    while executing
"lindex $coorList($i) ...

Originally posted by jianchaoyv at 2009-11-18 16:36:
我的问题运行.conf时，提示：
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: can't read "coorList(577)": no such element in array
    while executin ...

Originally posted by arthurii at 2009-12-6 14:03:
依照这个规定，那假设对象是核酸还有小分子的话，就需要另外自行定义polar和non polar了吧？

set numFrame [molinfo top get numframes]

for { set dt 1 } { $dt < $numFrame/2 } { incr dt } {
  set r2 0
  for { set fr0 1 } { $fr0 < $numFrame/2 } { incr fr0 } {
    set sel [atomselect top "water and name OH2 frame $fr0]
      foreach wti [$sel get index] {
         set wt0 [atomselect top "index $index" frame $fr0]
         set wtt [atomselect top "index $index" frame [expr $fr0 + $dt]]
         set cd0 [measure center $wt0]
         set cdt [measure center $wtt]
         set dr [veclength [vecsub $cdt $cd0] ]
         set r2 [expr $r2 + $dr*$dr]
         $wt0 delete
         $wtt delete
      }
      $sel delete
  }
  set dr2 [expr $r2/$n]
  puts "$n $dt\t$dr2"
}

Originally posted by zh1987hs at 2010-02-10 13:36:23:
想请问一下，当处理分子中带有杂原子的时候，比如FAD,或是金属原子的时候，它们的参数如何获得呢？看到VMD中有PARATOOL可以建立缺失原子类型的常数，但是在用的时候总出错，想问下楼主知道PARATOOL可以处理以上两 ...