[gmx-users] problem in simulation of dna-protein complex

[Mark Abraham]

nitu sharma wrote:
> Dear all ,
>                 I am doing simulation of DNA-protein complex.
>               Is anybody have idea about  .hdb of DNA  becoz in mannual 
> nothing is wrritten about DNA hydrogen database .I have edited The 
> database like this-
> ADE     9
> 2       6  H5*  C5*     C4*     O5*
> 1       5  H4*  C4*     O4*     C5*     C3*
> 1       5  H3*  C3*     C2*     C4*     O3*
> 1       5  H2*  C2*     C3*     C1*     O2`
> 1       2  H2`  O2`     C2*     C3*
> 1       5  H1*  C1*     N9      O4*     C2*
> 1       1  H2   C2      N1      N3
> 2       3  H6   N6      C6      C5
> 1       1  H8   C8      N9      N7
> 
> But when I run pdb2gmx command on DNA-protein pdb file the error comes 
> like this-
> Program pdb2gmx, VERSION 4.0.3
> Source code file: h_db.c, line: 96
> 
> Fatal error:
> Error in hdb file ffoplsaano.hdb:
> Wrong number of control atoms (3 iso 4) on line:
> 1       5  H4*     C4*     O4*     C5*   
>  
> If anybody have Idea what short of changes it needed please help me.

The hydrogen database format is described in chapter 5. The description 
is not a work of art, but you should start looking there.

Mark