[gmx-users] water clusters MD

[Mark Abraham]

----- Original Message -----
From: Oleksandr <nablaoblada at yahoo.com>
Date: Tuesday, June 1, 2010 12:43
Subject: Re: [gmx-users] water clusters MD
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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?

editconf -d 0.5 -f pentamer.pdb -o newbox.gro
genbox -cp newbox.gro -cs -o solvated.gro

You can get some more information with editconf -h and genbox -h.

Mark

> --- 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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> 
>       
> 
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