AMBER: pucker: deatails about pucker calculation

From: Vlad Cojocaru <>
Date: Fri, 28 Jan 2005 16:13:13 +0100

Dear all,
   If i use in ptraj "pucker puck :5.C1' :5.C2' :5.C3' :5.C4' :5.O4' out
pucker.dat" and in Carnal "PUCKER puck NUCLEIC 5" I get completely
different results. My residue should have a C2' endo sugar (meaning
about 144-180 degrees). So, from this point of view the Carnal
calculation seems the correct one while the ptraj seems wrong. Is it
possible to make ptraj give the same results as Carnal (as far as I know
both commands that I used - see above - for ptraj and carnal
calculations use the Altona convention, please correct me if I am wrong.
Thanks a lot for any advice

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Fri Jan 28 2005 - 15:53:00 PST
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