[gmx-users] water clusters MD

Oleksandr nablaoblada at yahoo.com
Tue Jun 1 03:38:40 CEST 2010


Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say I don't need it. Ok may be topology file can be written by hand, but what about "gro" file?

--- On Mon, 5/31/10, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] water clusters MD
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, May 31, 2010, 10:55 AM
> ----- Original Message -----
> From: Oleksandr <nablaoblada at yahoo.com>
> Date: Monday, May 31, 2010 18:48
> Subject: [gmx-users] water clusters MD
> To: gmx-users at gromacs.org
> 
> > Hi,
> > I'm new user of Gromacs. There are plenty examples how
> to do 
> > solvation study of various proteins. But I'd like to
> "solvate" 
> > highly ordered heavy water clusters in box of light
> water. At 
> > the first step when I execute  "pdb2gmx -f
> watercluster.pdb" I 
> > get an error no matter which model is chosen:
> >
> -------------------------------------------------------
> > 
> > Fatal error:
> > Atom H in residue HOH 4 not found in rtp entry with 3
> atoms
> >              while sorting atoms. Maybe
> different protonation state.
> >              Remove this hydrogen or choose a
> different 
> > protonation state.
> >              Option -ignh will ignore all
> hydrogens in the input.
> >
> -------------------------------------------------------
> > 
> > Can anybody help me how to solve this problem?
> 
> You're using a tool for a different job. pdb2gmx builds a
> topology file, mostly by constructing a [moleculetype] from
> a polymer of repeating units. Your moleculetypes are
> trivial, and at least one is already present in an .itp file
> for use with #include.
> 
> editconf and genbox make a box and fill it with generic
> solvent. It will be simplest to either write your .top by
> hand, or adapt an existing .top, depending what you mean by
> "heavy water". Either way, you'll need some fluency with
> GROMACS workflows and file types, so do all the general
> tutorial material you can find. If you'd done so, you might
> have realised that pdb2gmx is not really the tool for the
> job.
> 
> Mark
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