[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 ?
use the amber force field http://folding.stanford.edu/ffamber and
carefully follow the instructions there.
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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