[AMBER] question with pucker in six member ring

From: Ganesh Kamath <gkamath9173.gmail.com>
Date: Thu, 15 Oct 2009 15:55:45 -0400

Hi all,
I am trying to calculate the pucker in a six member ring. I use this lines
in ptraj

trajin data-0.00.crd
pucker name1 :233.C6 :233.C7 :233.N8 :233.C8A :233.C4A :233.N5 out
puckerDHPpseudo.dat cremer offset -90.0
pucker name2 :233.C6 :233.C7 :233.N8 :233.C8A :233.C4A :233.N5 out
puckerDHPamp.dat cremer amplitude offset -90.0
go


For the amplitude I get the output

      1.00 90.048991
      2.00 90.045684
      3.00 90.033221
      4.00 90.094447
      5.00 90.075243
      6.00 90.126185
      7.00 90.107877
      8.00 90.065907
      9.00 90.095487
     10.00 90.103874


and for pseudorotate

1.00 95.892046
      2.00 70.439829
      3.00 -150.576896
      4.00 171.025833
      5.00 165.689818
      6.00 152.105514
      7.00 142.713603
      8.00 -164.182655
      9.00 148.811860
     10.00 150.728189
     11.00 140.514928
     12.00 5.599644

Could some please help me understand this. thanks, ganesh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 15 2009 - 13:00:04 PDT
Custom Search