[gmx-users] DNA adduct simulation: grompp error

[Mark Abraham]

Nathalie Geneste wrote:
> Dear users,
> 
> I have some problems to launch a simulation with my molecular system 
> including 2 strands DNA + benzo[a]pyrene adduct.
> After some trials with default gromacs force fields, I downloaded 
> ffamber99.
> 
> I have 2 problems:
> 
> 1) my benzo[a]pyrene adduct is not recognized by ffamber99. Could you 
> propose me a force field compatible with my system ?

None of them, probably. You are very likely to have to parameterize your 
adduct. This is not trivial. See 
http://wiki.gromacs.org/index.php/Exotic_Species and/or 
http://wiki.gromacs.org/index.php/Parameterization

Mark