[gmx-users] water clusters MD

[Mark Abraham]

----- Original Message -----
From: Oleksandr <nablaoblada at yahoo.com>
Date: Tuesday, June 1, 2010 11:39
Subject: Re: [gmx-users] water clusters MD
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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 

You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file.

If you already have a .top for the original structure, genbox will update it suitably with the new waters. 

Mark

> 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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> 
> 
>       
> 
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