[gmx-users] DNA and GROMACS/GROMOS87

[Anton Feenstra]

John Kerrigan wrote:
> 
> Luke and Anton-
> 
> I've had success with DNA using the procedure that Anton described.  It's
> a pain, but just go and edit your file in a text editor that has a Find/Replace
>  command and make the appropriate substitutions.  Once you make the
> appropriate substitutions and make sure that the residue names are aligned
> in their proper columns in the PDB file (very important!), pdb2gmx will
> set everything up perfectly.

In stead of an interactive text editor you could use the 'sed' (which
stands for Streaming EDitor) command, as I indicated to automate it.

The command:
# sed 's/ A  /DADE/' input.pdb | sed 's/ G  /DGUA/' | \
  sed 's/ C  /DCYT/' | sed 's/ T  /DTHY/' > output.pdb
should do all you want. Note the spaces around 'A', 'G', etc.
I typed one before and two after, but I'm not completely sure
if that works (you can try none before and three after, or two 
before and one after, or perhaps even three before and nono after).

The real problem is that DNA is not supported, and at best only 
tolerated in Gromacs, mainly due to the simple fact that no-one 
of the developers (including me) has had any interest in DNA... 

That is to say that a lot of work remains to be done on implementing
nucl.acid specifics in pdb2gmx, and some analysis tools. Not to
mention force field development; I don't think any of the parameters
has been modified since the '80-ies... ;-{

> RNA is a different story.  GROMACS is missing several parameters for
> uracil in its parameter set.  This leads to all kinds of fun errors. I
> started working on this at the end of the summer, then classes started,
> etc.  I haven't had time to work on this problem. :(

Seeing the age of the other parameters, you should be able to simply
copy all missing things in RNA from the corresponding parameters in
DNA, at least to get a good first guess. Could still be a bit of work, 
though...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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