AMBER Archive (2006)

Subject: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Jun 28 2006 - 05:46:49 CDT

Dear amber community,
   
  I have been trying to determine phase angles of pseudorotations for ribose sugar residues of a DNA-drug complex.
  I have read the Altona et al. JACS(1972),94,8295 paper cited in the ptraj_pucker section of the AMBER v8 manual.
  What I would like to know is whether or not the following ptraj input command is OK to determine the phase angles of ribose sugar residue 1 taking the dihedral angle about C2'-C3' as the bases and the O4' atom as the fifth atom to constitute a pseudorotational angle.
   
  Here is my ptraj input :
   
  traj.in dna.binpos
  pucker res1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out phaseangle.out time 0.2
   
   
   
  best regards,
   
  jenk

                 
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