[gmx-users] pdb2gmx error

[TJ Piggot]

You do not want to use the ffgmx forcefield. For simulating DNA and protein 
i would use the amber force field. For more info on the ffamber ports see:

http://folding.stanford.edu/ffamber/

Tom

--On Wednesday, May 30, 2007 04:17:26 -0700 Alaguraj Veluchamy 
<alaguraj_v at yahoo.com> wrote:

> Dear gmx-users,
> I am trying to run a simulation of a pdb with DNA molecule.
> I have give gromacs force fied and the error i found was,
>
> There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms
>
>   chain  #res #atoms
>   1 'A'   162   1245
>   2 'B'   162   1245
>   3 'C'    21    417
>   4 'D'    21    428
>   5 'E'     6      6
>
> All occupancies are one
> Opening library file /usr/local/gromacs/share/top/ffgmx.atp
> Atomtype 52
> Reading residue database... (ffgmx)
> Opening library file ffgmx.rtp
> Residue 50Fatal error: Atom type OWT4 (residue HO4) not found in atomtype
> database
>
> Although there are posts to use the PRODRG, but it gives error that more
> than 300 atoms cannot be processed.
> i am able to do simulation the pdb without DNA.
> but with protein-dna complex it shows the above error.
> what may be the solution ?
> Regards,
> A.Raj
>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.