[gmx-users] NAGA

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Tue Aug 31 18:22:33 CEST 2010


Hello,

     I am trying to simulate N-methylglycine amide. I selected 'none'  
for the termini using oplsaa forcefield. I got the topology but I got  
the error saying:

ERROR 1 [file topol.top, line 126]:
   No default Ryckaert-Bell. types

I checked the line 126 in my topol file and it is the dihedral between  
the atoms C-C-C-N  (5 1 9 7). This is my PDB file:

ATOM      1  CA  NAGA    1       2.010  -3.420   3.690  1.00 20.00      
         C
ATOM      2 HA1  NAGA    1       2.621  -3.652   4.447  1.00 20.00      
         H
ATOM      3 HA2  NAGA    1       1.081  -3.720   3.908  1.00 20.00      
         H
ATOM      4 HA3  NAGA    1       2.321  -3.880   2.858  1.00 20.00      
         H
ATOM      5  CB  NAGA    1       2.020  -1.900   3.470  1.00 20.00      
         C
ATOM      6  OB  NAGA    1       2.720  -1.200   4.200  1.00 20.00      
         O
ATOM      7  NE  NAGA    1       1.270  -1.350   2.500  1.00 20.00      
         N
ATOM      8  HE  NAGA    1       1.280  -0.370   2.350  1.00 20.00      
         H
ATOM      9  CC  NAGA    1       0.360  -2.060   1.560  1.00 20.00      
         C
ATOM     10 HC1  NAGA    1      -0.410  -1.462   1.336  1.00 20.00      
         H
ATOM     11 HC2  NAGA    1       0.020  -2.891   2.000  1.00 20.00      
         H
ATOM     12  CD  NAGA    1       1.090  -2.440   0.270  1.00 20.00      
         C
ATOM     13  OD  NAGA    1       2.270  -2.810   0.300  1.00 20.00      
         O
ATOM     14  NB  NAGA    1       0.370  -2.340  -0.840  1.00 20.00      
         N
ATOM     15 HB1  NAGA    1       0.780  -2.570  -1.720  1.00 20.00      
         H
ATOM     16 HB2  NAGA    1      -0.580  -2.040  -0.790  1.00 20.00      
         H

Is there a way for me to determine that specific dihedral in .bon.itp file?

Nisha P




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