[gmx-users] pdb2gmx error

[Alaguraj Veluchamy]

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

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ALAGURAJ VELUCHAMY
c/o Dr.S.KRISHNASWAMY,
CENTRE OF  EXCELLENCE IN BIOINFORMATICS,
MADURAI KAMARAJ UNIVERSITY,
MADURAI, TN.
Ph:09486148690
       
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