[gmx-users] DNA topology

[K.A.Feenstra]

Dmitry Kovalsky wrote:
> Hi ALL
> My coworker wants to simulate DNA with protein but encountered some problems.
> pdb2gmx cann't convert nucleotides to gro format writing "Fatal error: Residue 
> 'A' not found in residue topology database" Renaming A, C, G, T to DADE, DGUA, 
> DCYT, DTHY result the same errors. Nucleotide topologies obtained from ProDrug 
> server donnt resolve the problem

First a disclaimer: DNA is not well-supported in GROMACS, and the status of
the actual force-field parameters is unclear. Use at your own descretion!

I think the DNA residues are named ADE, GUE, CYT and THY.
You can find that in ff*.rtp files.

-- 
Groetjes,

Anton
  ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
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