Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types?

From: 何毓辉 (he.yuhui.ime_at_gmail.com)
Date: Tue Sep 22 2009 - 02:51:56 CDT

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Dear all,

    Right now, I employed NAMOT to generate PDB files of DNA with wanted
sequence, and then generate corresponding PSF files via
top_all27_prot_na.inp. The obtained PSF files are as follows:

     383 !NATOM
       1 ADNA 1 ADE C4' CN7 0.160000 12.0110 0
       2 ADNA 1 ADE H4' HN7 0.090000 1.0080 0
       3 ADNA 1 ADE O4' ON6 -0.500000 15.9994 0
       4 ADNA 1 ADE C1' CN7B 0.160000 12.0110 0
       5 ADNA 1 ADE H1' HN7 0.090000 1.0080 0

  Then, I have to use cornell.prm as parameter file in NAMD simulation. I
found that the naming rules of atom type in top_all27_prot_na.inp are
different from that in cornell.prm.
   I guess that for topology file, the atom types (CN7, HN7, ON6...) are
named in Charmm format, while are named in Amber format for parameter file--001636b14b3b55b662047425df1d--

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