[gmx-users] (no subject)

Patel Ronak Y ronakp at iitb.ac.in
Tue Apr 27 17:47:00 CEST 2004

Hi all,

I am simulating six heptapeptides as a different chains in water. The N
terminus has -CO-CH3 and the C-terminus has NH-CH3.The simulation works
well but when I use xrama and g_rama to check dihedral angles. I get the
following error.

Dihedral X, Y not found in topology. (X,Y are the numbers of O of -CO of
7th residue and Y is the number of H of NAC as mention in the .top file
created by pdb2gmx)

Everything works nicely with one heptapeptide.

These are my topology of extra groups that I have introduced in the

[ ACE ]
 [ atoms ]
    CA   CH3   0.000     0
     C     C   0.380     1
     O     O  -0.380     1
 [ bonds ]
     C    CA   gb_26
     C     O   gb_4
     C    +N   gb_9
 [ angles ]
   CA     C    +N    ga_18
    O     C    +N    ga_32
   CA     C     O    ga_29
 [ impropers ]
    C    CA    +N     O    gi_1
 [ dihedrals ]
   CA  C  +N  +CA  gd_4

[ NAC ]
 [ atoms ]
    N   N   -0.280  0
    H   H    0.280  0
    CA  CH3  0.000  1
 [ bonds ]
    N   H    gb_2
    N   CA   gb_20
 [ angles ]
   -C   N   H   ga_31
    H   N   CA  ga_17
   -C   N   CA  ga_21
 [ impropers ]
    N  -C   CA   H   gi_1
 [ dihedrals ]
    -CA -C  N  CA  gd_4

Can somebody plz tell me where is the error.

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