[gmx-users] pdb2gmx error
alaguraj_v at yahoo.com
Wed May 30 13:17:26 CEST 2007
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
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 ?
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