[gmx-users] Virtual sites error

[Timofey Tyugashev]

Trying to add hydrogen virtual sites to the model (using -vsites h 
option in pdb2gmx) results in a salvo of error messages when running 
grommp to create .tpr file after the solvation:

ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
   No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
   No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two 
MCH3 and one MC atoms, which should serve (the way I understand the 
situation) as replacement methyl group in thymine. There are several 
more pairs of same errors corresponding to different thymine methyl 
groups in the DNA strands.

Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  ai    aj funct            c0            c1
     2     3     2
   110   111     2
   110   112     2
   111   112     2

[ atoms ]

    110         CM    321     DT     C5    110     0.0025 12.01   ; qtot 
-2.867
    111       MCH3    321     DT   MC71    111          0 7.517   ; qtot 
-2.867
    112       MCH3    321     DT   MC72    111          0 7.517   ; qtot 
-2.867