[gmx-users] problem simulating DNA

[Manish Datt]

hello everybody

i had sent this mail before but was not accepted because of a large
attachemnt (top file). now i`m sending it again without any attachment.

i`m trying to simulate a double helical DNA using gromacs 3.3 with G43a1
force field. for this i modified the residue names in the pdb file and
converted the file the gromacs format using pdb2gmx command. then i set
the simulation box using editconf. now on preprocessing the files with
grompp i`m getting following error
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
WARNING 1 [file "1blo_dna_p2g.top", line 4832]:
  No default Proper Dih. types, using zeroes
WARNING 2 [file "1blo_dna_p2g.top", line 4849]:
  No default Proper Dih. types, using zeroes
WARNING 3 [file "1blo_dna_p2g.top", line 4866]:
  No default Proper Dih. types, using zeroes
WARNING 4 [file "1blo_dna_p2g.top", line 4883]:
  No default Proper Dih. types, using zeroes
WARNING 5 [file "1blo_dna_p2g.top", line 4900]:
  No default Proper Dih. types, using zeroes
WARNING 6 [file "1blo_dna_p2g.top", line 4916]:
  No default Proper Dih. types, using zeroes
WARNING 7 [file "1blo_dna_p2g.top", line 4932]:
  No default Proper Dih. types, using zeroes
WARNING 8 [file "1blo_dna_p2g.top", line 4948]:
  No default Proper Dih. types, using zeroes
WARNING 9 [file "1blo_dna_p2g.top", line 4965]:
  No default Proper Dih. types, using zeroes
WARNING 10 [file "1blo_dna_p2g.top", line 4982]:
  No default Proper Dih. types, using zeroes
Cleaning up temporary file gromppMWjN6A
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: fatal.c, line: 416

Fatal error:
Too many warnings, grompp terminated
-------------------------------------------------------

googling through the mail archive i found that prodrg server might help.
but i not sure which of the output file generated by the server to be
used and how exactly to use them since the another strange thing about
the pdb files generated by prodrg output is that it changes the
residues names and also represents the ATOM as HETATM.

kindly help me solve this problem

best regards,


Manish Datt
Research Scholar
Bioinformatics Centre
Institute of Microbial Technology
Sector 39A, Chandigarh-160036
India.