[gmx-users] Dummy Problem.

Anthony Cruz acb15885 at uprm.edu
Tue Feb 6 13:25:32 CET 2007

Hi Users:

I have a question about dummy atoms. I try to simulate a protein that have a 
cysteine modified with a NO group. I found a NO model that have 3 sites, one 
at each atom and other in the center of mass (Biophys. Chem. 98 (2002) 183). 

[ SNC ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   SG     S     0.00000     1
   ND   NON    -0.25000     2
  CON   COM     0.59500     2
   OE   NOO    -0.34500     2
    C     C       0.380     3
    O     O      -0.380     3
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    SG    gb_30
   SG    ND    gb_49
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    SG     ga_15
   CB    SG    ND     ga_47
   SG    ND    OE     ga_48
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    SG     gd_17
   CA    CB    SG    ND     gd_13
   CB    SG    ND    OE     gd_22

In my topology before all the bonded information I add the following lines 
with the appropiate numbers:

 [ dummies2 ]
;Dummy      from       funct    a
  CON    ND    OE       1       0.064381

[ constraint ]
;  ai  aj funct           b0
ND      OE	2	   0.12032

The problem is that the dummy colapse with the ND atom during the EM.  What 
could be the problem?  I need to add the dummies2 section in my topology if 
it is present in the residue topology and it is present in my pdb???



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