[gmx-users] ERROR No default G96Angle types

Villarealed villarealed at hss.edu
Fri Mar 1 21:49:05 CET 2013


Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids. 
When I tried to add ions to the virtual box
I obtained these error

ERROR 1 [file topol.top, line 566]:
  No default G96Angle types
ERROR 2 [file topol.top, line 801]:
  No default Proper Dih. types

The second error  was resolved by modified the archive "residuetypes.dat". 
I only add this line "SEP     Protein"
To be honest I don't know how to resolve the ERROR 1.
If someone could help me I will appreciate.
Eduardo 

 
grompp -f ions.mdp -c newbox_solv.gro -p topol.top -o ions.tpr

ERROR 1 [file topol.top, line 566]:
  No default G96Angle types

topol.top

[ angles ]
;  ai    aj    ak funct            c0            c1            c2           
c3
    1     2     3     2 

newbox_solc.gro
    1ACE     CA    1   2.759   1.040   1.830
    1ACE      C    2   2.881   1.130   1.839
    1ACE      O    3   2.988   1.083   1.878
    2SER      N    4   2.872   1.258   1.805

aminoacids.rtp
[ 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
 [ impropers ]
    C    CA    +N     O    gi_1 

ERROR 2 [file topol.top, line 801]:
  No default Proper Dih. types

topol.top
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2           
c3            c4            c5
   72    71    73    74     1
   H     N     CA    CB              
newbox_sol.gro
   10SEP      N   71   2.348   2.562   2.883
   10SEP      H   72   2.446   2.556   2.863
   10SEP     CA   73   2.260   2.594   2.768
   10SEP     CB   74   2.186   2.467   2.720
   10SEP     OG   75   2.110   2.424   2.827
   10SEP      P   76   2.001   2.314   2.797
   10SEP    O1P   77   2.066   2.200   2.732
   10SEP    O2P   78   1.949   2.275   2.928
   10SEP    O3P   79   1.895   2.372   2.710
   10SEP      C   80   2.164   2.714   2.789
   10SEP      O   81   2.051   2.714   2.741

aminoacids.rtp
[ SEP ]tar -zcvf prog-1-jan-2005.tar.gz /home/jerry/prog
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     2
   OG    OA    -0.36000     2
    P     P     0.94000     2
  O1P    OP    -0.86000     2
  O2P    OP    -0.86000     2
  O3P    OP    -0.86000     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    OG    gb_17   
   OG     P    gb_27    
    P   O1P    gb_23    
    P   O2P    gb_23    
    P   O3P    gb_23    
 [ 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    OG     ga_12   
   CB    OG     P     ga_25
   OG     P   O1P     ga_13
   OG     P   O2P     ga_13
   OG     P   O3P     ga_13
  O1P     P   O2P     ga_28
  O1P     P   O3P     ga_28
  O2P     P   O3P     ga_28
 [ 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    OG     gd_17   
   CA    CB    OG     P     gd_14   
   CB    OG     P   O1P     gd_11





-----
Eduardo Villarreal Ramírez   
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.                            


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