AMBER Archive (2009)

Subject: [AMBER] question with pucker in six member ring

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Thu Oct 15 2009 - 14:55:45 CDT

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_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_N5 out
puckerDHPpseudo.dat cremer offset -90.0
pucker name2 :233_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_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
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