[gmx-users] pdb2gmx

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
> 
> > If you have a system whit protein and 'other' molecules, you can always
> > process them in pdb2gmx separately, and put the .top and .gro files
> > together manually (takes some puzzling, though).
> 
> I ment that I would like to see pdb2gmx do the puzzling for me :)
> Sinve it doesn't, the solution would be, as Berk said, to translate my
> .top into a ff***.rtp entry. That would still require some puzzling, but
> only once.

That doesn't make much sense to me. If you get something out of pdb2gmx, 
you must already have an .rtp entry for the molecule.

As you might already have ready before on the list, a good starting
point 
for creating a novel topology is the PRODRG server, but my experience is 
that sometimes for small molecules it is easier done by hand (or maybe I
am a bit too suspicious of things I didn't write myself... ;-).

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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