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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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