[gmx-users] Prodrg

[Rodrigo Reston]

Ok. The molecule I'm trying to get the coordinates and
topology for is a naphthalene derivative to which an
amino or nitro group may be bonded in the position 4 ,
or not. So, I'd like to have 3 computer models with
which I could work in molecular dynamics simulations.
None of the .top files available in the Prodrg server
worked - first, I should have asked what was I
supposed to do with the topology file .itp found in
the Docking / MD simulations for Gromacs.
Rodrigo S. Reston, BSc.
UFMG, Brazil.

--- David <spoel at xray.bmc.uu.se> wrote:

> On Fri, 2005-10-14 at 12:32 -0700, Rodrigo Reston
> wrote:
> > Just expanding my previous e-mail:
> > Hi. I used Prodrg server to create the coordinates
> > and topology for a molecule. None of the .top
> files
> > available at the server, after I make the run,
> > work. [ I cannot create a .top using x2top because
> Please be more specific on what kind of molecule,
> and what you mean with
> does not work.
> 
> 
> > there's a problem in the .gro file - it always
> > complains about the FF not having the type for
> some
> > atom in the structure that's forming illegal bonds
> -
> > even if I change the molecule just a bit. I have
> no
> > idea what to do with the .itp file. ] And I cannot
> > generate a .top file using the .pdb file through
> > pdb2gmx because Gromacs does not recognize the
> "DRG"
> > residue!
> > I sorry, I thought I could be more specific but I
> > can't. 
> > 
> > 
> > 	
> > 		
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> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  
> http://xray.bmc.uu.se/~spoel
>
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