From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jun 20 2010 - 08:55:26 CDT
Nothing is duplicated - they have different multiplicities. The appendix of
the NAMD tutorial has an explanation of the dihedral parameters:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node2
3.html
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of BIN ZHANG
Sent: Friday, June 18, 2010 12:42 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: phosphate parameters
Hi, there:
While looking at the ADP parameters in the file "par_all27_na.prm", I
found a lot of duplicate entries for the dihedral angles (see
attached). Is this a mistake or on purpose? I was trying to convert
this to other format, and would like to know which one I should use.
Thank you very much,
BIn
=====================================================
928 P2 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr.
7/95
929 P2 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
930 P ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
931 P ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
932 P2 ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
933 P2 ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
934 P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
935 P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
936 P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
937 P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
938 P ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
939 P ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
940 P2 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
941 P2 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
942 P2 ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm
jr. 7/95
943 P2 ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm
jr. 7/95
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