[gmx-users] water clusters MD

[Oleksandr]

It would be helpful if you could be more specific. For example, the standard procedure described in tutorial:

pdb2gmx -f input.pdb
edit conf -f conf.gro d 0.5 -o newbox.gro
genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb

Now, could you please illustrate how would you do this for "trivial" non-protein molecules?


--- On Tue, 6/1/10, 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: Tuesday, June 1, 2010, 4:16 AM
> ----- 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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