[gmx-users] pdb2gmx error
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 30 13:50:10 CEST 2007
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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