[gmx-users] No default U-B types in CHARMM36 FF

[Albert]

Hello:

I am running command:

grompp -f em.mdp -c ion-em.pdb -o test.tpr


but it failed with messages:



-----------------------------------------------------------------------------------------------------

Generated 71611 of the 71631 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 45719 of the 71631 1-4 parameter combinations

ERROR 1 [file topol.top, line 22781]:
   No default U-B types

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/src/kernel/grompp.c, line: 1610

Fatal error:
There were 13 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------



I checked the line 22781, it was the last line of following:

[ angles ]
;  ai    aj    ak funct            c0            c1 c2            c3
     2     1     3     5
     2     1     4     5  (<---this line)



Here is my initial residues:


[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
; residue  36 GLY rtp GLY  q  0.0
      1        NH2     36    GLY      N      1      -0.96 14.007   ; 
qtot -0.96
      2          H     36    GLY    HT1      2       0.34 1.008   ; qtot 
-0.62
      3          H     36    GLY    HT2      3       0.34 1.008   ; qtot 
-0.28
      4        CT2     36    GLY     CA      4        0.1 12.011   ; 
qtot -0.18
      5        HB2     36    GLY    HA1      5       0.09 1.008   ; qtot 
-0.09
      6        HB2     36    GLY    HA2      6       0.09 1.008   ; qtot 0
      7          C     36    GLY      C      7       0.51 12.011   ; 
qtot 0.51
      8          O     36    GLY      O      8      -0.51 15.999   ; qtot 0
; residue  37 SER rtp SER  q  0.0
      9        NH1     37    SER      N      9      -0.47 14.007   ; 
qtot -0.47
     10          H     37    SER     HN     10       0.31 1.008   ; qtot 
-0.16
     11        CT1     37    SER     CA     11       0.07 12.011   ; 
qtot -0.09
     12        HB1     37    SER     HA     12       0.09 1.008   ; qtot 0
     13        CT2     37    SER     CB     13       0.05 12.011   ; 
qtot 0.05
     14        HA2     37    SER    HB1     14       0.09 1.008   ; qtot 
0.14
     15        HA2     37    SER    HB2     15       0.09 1.008   ; qtot 
0.23
     16        OH1     37    SER     OG     16      -0.66 15.999   ; 
qtot -0.43
     17          H     37    SER    HG1     17       0.43 1.008   ; qtot 0
     18          C     37    SER      C     18       0.51 12.011   ; 
qtot 0.51
     19          O     37    SER      O     19      -0.51 15.999   ; qtot 0
; residue  38 PRO rtp PRO  q  0.0
     20          N     38    PRO      N     20      -0.29 14.007   ; 
qtot -0.29
     21        CP3     38    PRO     CD     21          0 12.011   ; 
qtot -0.29
     22        HA2     38    PRO    HD1     22       0.09 1.008   ; qtot 
-0.2
     23        HA2     38    PRO    HD2     23       0.09 1.008   ; qtot 
-0.11
     24        CP1     38    PRO     CA     24       0.02 12.011   ; 
qtot -0.09
     25        HB1     38    PRO     HA     25       0.09 1.008   ; qtot 0
     26        CP2     38    PRO     CB     26      -0.18 12.011   ; 
qtot -0.18
     27        HA2     38    PRO    HB1     27       0.09 1.008   ; qtot 
-0.09
     28        HA2     38    PRO    HB2     28       0.09 1.008   ; qtot 0
     29        CP2     38    PRO     CG     29      -0.18 12.011   ; 
qtot -0.18
     30        HA2     38    PRO    HG1     30       0.09 1.008   ; qtot 
-0.09
     31        HA2     38    PRO    HG2     31       0.09 1.008   ; qtot 0
     32          C     38    PRO      C     32       0.51 12.011   ; 
qtot 0.51
     33          O     38    PRO      O     33      -0.51 15.999   ; qtot 0
; residue  39 GLY rtp GLY  q  0.0
     34        NH1     39    GLY      N     34      -0.47 14.007   ; 
qtot -0.47
     35          H     39    GLY     HN     35       0.31 1.008   ; qtot 
-0.16
     36        CT2     39    GLY     CA     36      -0.02 12.011   ; 
qtot -0.18
     37        HB2     39    GLY    HA1     37       0.09 1.008   ; qtot 
-0.09
     38        HB2     39    GLY    HA2     38       0.09 1.008   ; qtot 0
     39          C     39    GLY      C     39       0.51 12.011   ; 
qtot 0.51
     40          O     39    GLY      O     40      -0.51 15.999   ; qtot 0


I used command:

pdb2gmx -f p.pdb -o gmx.pdb -ter

to generate the topology file, and I assinged: GLY-NH2 for the first 
residue GLY, -COOH for the last residue.

thank you very much.

best
Albert