VMD-L Mailing List

From: mashaojie163 (mashao_jie_at_163.com)
Date: Fri Oct 08 2004 - 07:28:20 CDT


----- Original Message -----
From: mashaojie163
To: vmd-l
Sent: Tuesday, September 28, 2004 12:12 PM
Subject: vmd-l: measure fit error??


Hello:
   I want to calculate the rmsd of protein by use of snopshots during MD simulation. when I regard the frame 0 as base strusture.
   for example:
   

   set sel0 [atomselect top "protein and backbone and noh" frame 0]
   set sel1 [atomselect top "protein and backbone and noh" frame 1]
   set sel2 [atomselect top "protein and backbone and noh" frame 2]
   measure fit $sel0 $sel1
   the return value is {1.0 0.0 0.0 1.#QNAN} {0.0 1.0 0.0 1.#QNAN} {0.0 0.0 1.0 1.#QNAN} {0.0 0.0 0.0 1.#QNAN}
   measure fit $sel1 $sel0
  the return value is -1.#IND -1.#IND -1.#IND -1.#IND} {-1.#IND -1.#IND -1.#IND -1.#IND} {-1.#IND -1.#IND -1.#IND -1.#IND} {-1.#IND -1.#IND -1.#IND -1.#IND}
  measure fit $sel2 $sel1
 the return value is right {0.999995708466 0.000757500936743 0.00282854191028 0.0485077947378} {-0.000757581554353 0.999999701977 2.7410878829e-005 -0.0505107417703} {-0.00282852025703 -2.95536119665e-005 0.999996006489 0.00872712116688} {0.0 0.0 0.0 1.0}

I don not know what do "-1.#QNNA" and "-1.#IND" mean? why these appear when selection including frame 0?
  
Best Regards
                          Ma shaojie