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

[Simon Kit Sang Chu]

Hi everyone,

I have a list of short peptides generated from PyMOL. I am ignoring all the
hydrogen atoms and use neutral terminal caps for both ends. All seems fine
from pdb2gmx to solvation. The problem kicks in when I add ions.

*Here was what I did - *


   1. pdb2gmx
   2. editconf
   3. solvate
   4. grompp ions.mdp < Error kicks in.

*grompp error :*

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

*ALA-GLY-GLY-PRO.top :*

   30    38    40     5                  ( line 293 - bond angle )

  27    26    30    38     9           ( line 367 - dihedrals )

*ALA-GLY-GLY-PRO.gro :*
    5PRO      N   26   2.595   2.395   0.998
    5PRO     CD   27   2.565   2.536   0.983
    5PRO    HD1   28   2.479   2.558   1.029
    5PRO    HD2   29   2.557   2.559   0.886
    5PRO     CA   30   2.731   2.366   1.042
    5PRO     HA   31   2.772   2.294   0.987
    5PRO     CB   32   2.799   2.503   1.026
    5PRO    HB1   33   2.871   2.515   1.094
    5PRO    HB2   34   2.838   2.514   0.935
    5PRO     CG   35   2.685   2.603   1.049
    5PRO    HG1   36   2.669   2.617   1.147
    5PRO    HG2   37   2.705   2.691   1.006
    5PRO      C   38   2.734   2.314   1.186
    5PRO    OT1   39   2.629   2.300   1.250
    5PRO    OT2   40   2.856   2.283   1.238

Interestingly, only several peptides are affected. Many others are not
affected -

ALA-GLY-GLY-PRO
GLY-PRO-ALA-PRO
ALA-PRO-ALA-ALA
GLY-ALA-ALA-PRO
ALA-PRO-ALA-GLY
ALA-PRO-SER-THR

...

Sometimes bond angle is affected, but dihedral is always involved. The
error always associates with the ends. I believe there has to be something
to do with the capping. Has anyone experienced this before?

Regards,
Simon