[gmx-users] Virtual sites error

[Erik Marklund]

Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:
> 
> 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
> -- 
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