[gmx-users] No default Proper Dih. types when using neutral terminal

[Simon Kit Sang Chu]

Hi everyone,

Last time, I mentioned missing parameter for neutral terminal dihedral and
U-B type. After some debugging, I am still not sure what the cause was. I
hope providing more information could help to resolve the issue. I am using
CHARMM36 forcefield.

Brief summary of the problem -
No dihed. parameter / U-B types after using neutral terminals

Command I ran -

   1. gmx pdb2gmx -f ALA-GLY-GLY-PRO. pdb -o ALA-GLY-GLY-PRO.gro -p
   ALA-GLY-GLY-PRO.top -i ALA-GLY-GLY-PRO.itp -water tip3p -ignh -ter
   Choose CHARMM36 all-atom force field (November 2016), NH2 and COOH
   terminals
   2. gmx editconf -f ALA-GLY-GLY-PRO.gro -o ALA-GLY-GLY-PRO-box.gro -c -d
   0.8 -bt dodecahedron
   3. gmx solvate -cp ALA-GLY-GLY-PRO-box.gro -cs spc216.gro -o
   ALA-GLY-GLY-PRO-solvated.gro -p ALA-GLY-GLY-PRO.top
   4. gmx grompp -f ions.mdp -c ALA-GLY-GLY-PRO-solvated.gro -p
   ALA-GLY-GLY-PRO.top -o ions.tpr

Fatal error in grompp -


ERROR 1 [file ALA-GLY-GLY-PRO.top, line 293]:
  No default U-B types

ERROR 2 [file ALA-GLY-GLY-PRO.top, line 367]:
  No default Proper Dih. types

Meanwhile in the topology file -

[ angles ]

   30    38    40     5          ( line 293 )


[ dihedral ]

   27    26    30    38     9  ( line 367 )

; residue   5 PRO rtp PRO  q  0.0
    26          N      5    PRO      N     26      -0.29     14.007   ;
qtot -0.29
    27        CP3      5    PRO     CD     27          0     12.011   ;
qtot -0.29
    28        HA2      5    PRO    HD1     28       0.09      1.008   ;
qtot -0.2
    29        HA2      5    PRO    HD2     29       0.09      1.008   ;
qtot -0.11
    30        CP1      5    PRO     CA     30       0.02     12.011   ;
qtot -0.09
    31        HB1      5    PRO     HA     31       0.09      1.008   ;
qtot 0
    32        CP2      5    PRO     CB     32      -0.18     12.011   ;
qtot -0.18
    33        HA2      5    PRO    HB1     33       0.09      1.008   ;
qtot -0.09
    34        HA2      5    PRO    HB2     34       0.09      1.008   ;
qtot 0
    35        CP2      5    PRO     CG     35      -0.18     12.011   ;
qtot -0.18
    36        HA2      5    PRO    HG1     36       0.09      1.008   ;
qtot -0.09
    37        HA2      5    PRO    HG2     37       0.09      1.008   ;
qtot 0
    38         CD      5    PRO      C     38       0.72     12.011   ;
qtot 0.72
    39         OB      5    PRO    OT1     39      -0.55    15.9994   ;
qtot 0.17
    40        OH1      5    PRO    OT2     40      -0.61    15.9994   ;
qtot -0.44
    41          H      5    PRO    HT2     41       0.44      1.008   ;
qtot 0


I further check if angle type between CP1, CD and OH1 exists in ffbond.itp.
Indeed there is no such angle.  Maybe there is something wrong when using
NH2 and COOH terminals?

Please feel free to give any suggestion. I appreciate any comment.

Regards,
Simon