[gmx-users] dihedrals again

Andrea Muntean andreamuntean at gmail.com
Tue Oct 28 11:48:37 CET 2008

Hi all,

I did some work on thise dihedrals for polystyrene, and I simplified
my version now, using also the inspiration from PHE residue.
My problem now is that for the dihedral around the CH2-CH bond in the
inner monomer (PS thus) I define in the rtp

-CH     CH2     CH      +CH2    gd_17

but in the top fileinstead of
2   9   10   17   gd_17

 I get this:

2   9   10   11   (without any parameter).

This make me think that pdb2gmx does not count the dihedral as I
defined it (why?) but puts a "default" dihedral there, without any
parameter. I am right? What would be a solution for that?

My dihedrals are now defined as follows (it helps if you really draw
the molecule):

the entries in the rtp file for first (PS1), inner (PS) and last (PSN) monomer:


;in the chain - 3-fold (n=3)
CH3     CH      +CH2    +CH     gd_17
;around CH-CB - 2-fold (n=2)
CH3     CH      CB      CG5     gd_1


;in the chain - 3-fold
CH2     CH      +CH2    +CH     gd_17
-CH     CH2     CH      +CH2    gd_17
;around CH-CB - 2-fold
CH2     CH      CB      CG5     gd_1


;in the chain - 3-fold (n=3)
-CH     CH2     CH      CH3     gd_17
;around CH-CB - 2-fold (n=2)
CH2     CH      CB      CG5     gd_1

The results for trimer in the top file.
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    1     2     3     8     1    gd_1
    1     2     9    10     1    gd_17
    2     9    10    11     1
    9    10    11    16     1    gd_1
    9    10    17    18     1    gd_17
   10    17    18    25     1    gd_17
   17    18    19    24     1    gd_1

Best regards,

More information about the gromacs.org_gmx-users mailing list