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.C1' :1.C2' :1.C3' :1.C4' :1.O4' out phaseangle.out time 0.2
best regards,
jenk
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Received on Sun Jul 02 2006 - 06:07:05 PDT
