paricle type in residue based coarse graining of NAMD

From: Yongcheng Zhou (yzhou_at_math.colostate.edu)
Date: Mon Jun 23 2014 - 14:37:16 CDT

Hi there, I wanted to do some analysis of interaction potential energies
among residues/side chains using residue based coarse graining, but was
confused by the various particle types defined in the psf file. For
example, we can see such a section in a psf file,

        1 P1 55 SER BAS QDC 1.000000 72.0000 0
        2 P1 55 SER SID P1S 0.000000 72.0000 0
        3 P1 56 THR BAS NDH 0.000000 72.0000 0
        4 P1 56 THR SID P1T 0.000000 72.0000 0
        5 P1 57 PHE BAS N0H 0.000000 72.0000 0
        6 P1 57 PHE SI1 SC4F 0.000000 45.0000 0
        7 P1 57 PHE SI2 SC4F 0.000000 45.0000 0
        8 P1 57 PHE SI3 SC4F 0.000000 45.0000 0

and I need to compute the bonded, angular, and other interactions. The original
MARTINI article (JCTC, V4, P819-834, 2008) says that only a small
set of parameters are used for these interactions, and they depend on the
kind of secondary structure of the backbone particle. So my question is

(1) How to determine the secondary structure of the base of a coarse grained
residue (coil/helix/turn/bend/extended)?

or

(2) how to infer the secondary structure from the particle names of these
residues in the above psf file? For example, What are the
secondary structures of the particles QDC/NDH/N0H in the above psf file?

Thank you very much!

-yc

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