[gmx-users] GROMACS nucleic acid sim. using GROMOS87

[K.A. Feenstra]

Luke Czapla wrote:
>  Hi,
> 
>   I'm trying to simulation a nucleic acid/protein system using the
> standard GROMOS87 (default united atom) force field in GROMACS.  I want to
> change the residue identifiers from DADE for adenine in DNA to just A (the
> convention in PDB files for nucleic acids) in the GROMOS87 implementation,
> 
>   I tried to do this by editing ffgmx.rtp (in /usr/share/gromacs/top from
> the RPM distribution package - we're in linux) and changing the [ DADE ]
> to [ A ] but it still thinks DADE is the correct terminology.  I was
> wondering if anyone knows what I am doing wrong and what issues are
> involved in the nucleic acid simulations using GROMACS.

There has been some discussion on DNA on this list, but not much. In particular,
I remember hearing about problems, but not (many) solutions... ;-(

As for the residue naming; IIRC pdb2gmx has some of these names hardcoded.
Yes, I know, that is not nice. Try renaming your DNA residues in the .pdb
file in stead. If you want it automated, running:
# sed 's/ A  /DADE/' my.pdb >! new.pdb
should do the trick, repeat for any other names...

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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