[gmx-users] water clusters MD

Mark Abraham mark.abraham at anu.edu.au
Mon May 31 10:55:50 CEST 2010

----- 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.


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