[gmx-users] pdb2gmx error

[David van der Spoel]

Alaguraj Veluchamy 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
> 
use the amber force field http://folding.stanford.edu/ffamber and 
carefully follow the instructions there.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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