AW: paricle type in residue based coarse graining of NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 24 2014 - 03:13:21 CDT

See the fix_martini_psf.tcl script which actually applies the backbone bead
type by the all-atom secondary structure used to build the CG model.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Yongcheng Zhou
> Gesendet: Montag, 23. Juni 2014 16:14
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: paricle type in residue based coarse graining of NAMD
>
>
> Hi there, I want 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 the 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 that depends 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
> residue in the above psf file? For example, What QDC/NDH/N0H stand for
> in
> the above psf file?
>
> Thank you very much!
>
> -yc

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