[gmx-users] problem simulating DNA

[Maik Goette]

Hi

This isn't much information, but I guess, those problems may occur due 
to the termini (and their missing FF-entries(?)) of the DNA.
At first, you should have a look at the top-file and find out, which 
bases/atoms are responsible for the warnings. Then have a look, if the 
dihedral simply isn't defined in the bon.itp.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Manish Datt wrote:
> 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.
> 
> 
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