[gmx-users] Creation of a Non-Standard Residue

Mark Abraham mark.abraham at anu.edu.au
Fri Jun 4 04:02:58 CEST 2010

----- Original Message -----
From: Mark Abraham <mark.abraham at anu.edu.au>
Date: Friday, June 4, 2010 11:51
Subject: Re: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> ----- Original Message -----
> From: Mark Zottola <mzottola at gmail.com>
> Date: Friday, June 4, 2010 10:40
> Subject: Re: [gmx-users] Creation of a Non-Standard Residue
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Let me clarify.>  >  >  > I have no problem determining the bond stretching or angle bending parameters for HCN.  This was a very straightforward task.  Unit conversion to get those values in a gromacs force field was also a non-issue.>   >  >  > The problems I am having are:>  >  >  > 1) How do I specify a POLAR hydrogen on a carbon atom?  There are polar hydrogens (or so it seems) in the gromacs forcei field, but ostensibly they are on heteroatoms such as nitrogen or oxyen.  Is there a way to force gromacs to let a polar hydrogen on a carbon?

Perhaps I misinterpreted this the first time. Of course all-atom forcefields have polar hydrogens. It seems your problem is that you can't make PRODRG produce an .itp suitable for ffgmx for HCN, because it assumes H bonded to C is non-polar. If so, then you have a potentially tricky problem and need to consult the documentation of that tool. Such a problem exists before GROMACS gets involved, so your second question seems misformed - GROMACS will do whatever you tell it, if that is consistent with the force field you're using.

> ffgmx has been deprecated for years (as pdb2gmx tells users), so you'll find it hard to interest people with this problem. PRODRG beta works for one of the GROMOS forcefields, however. The general issue is that you're trying to develop an all-atom model, so you need to target an all-atom forcefield.
>  > 2) I AM looking for advice on the van der Waals parameters.  Yes, I can guess and tweak until the cows come home, but obviously there are recommendations which I do not know.  So... any suggestions on this.>  >  >  > 3)  The problem is quite simple, I want to develop parameters for HCN so I can use it as both ligand AND as a component n a solvent box.  I do have the formula (4 or 5 steps from the web) to create my solvent box, but I need to have HCN properly parameterized.  >   >  >  > 4)  I am asking for this as I cannot use the Dundee server to make the appropriate topology file.>  >  >  > The warning blurb was good at saying "Parameter development is done by professionals, so please do not try this at home."  I am asking for help in the above issues as I am new to GROMACS but NOT other MD programs.> 
> Well, then you'll know how to follow up on the concrete advice there - start by reading the literature for the force field of interest to see how VDW parameters were derived. How best to follow up is strongly problem- and forcefield-dependent. You might decide the path of least resistance is to use an AMBER forcefield in GROMACS so that you can use AMBERTools automated parameterization tools.
> Mark > -- 
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