[gmx-users] multichain peptide simulation

Susan Idiula susan19 at iitb.ac.in
Wed May 5 12:20:01 CEST 2004


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

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

Everything works nicely with one heptapeptide.

These are the topology of the 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

I have 7 residues per chain, so in principle I should be getting 7x6 =42
phi-psi combinations, but xrama calculates 47 phi-psi combinations. i
presume it has to do something with the ends of each chain, but i am not

i have tried removing the extra CO-CH3 AND NH-CH3, but it didnot work.

any suggestions?


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