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

Mark Zottola mzottola at gmail.com
Fri Jun 4 02:38:57 CEST 2010

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?

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.

Thanks again for any help.

On Thu, Jun 3, 2010 at 7:30 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Mark Zottola <mzottola at gmail.com>
> Date: Friday, June 4, 2010 1:55
> Subject: [gmx-users] Creation of a Non-Standard Residue
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > I am trying to to create a non-standard residue - HCN.  This cannot be
> done by the Dundee PRODRG server as it subsumes the polar hydrogen into the
> carbon.  This results in a diatomic molecule that the program cannot handle.
> >
>  > I do mind creating a new drug by hand, but a search through the email
> list has been less than fruitful.  I have done parameter/non-standard
> residue formation in AMBER, I believe I understand the process.  Yet, there
> is no clear delineation of how one does charges.  The best I found was the
> proper suggestion that CHELPG charges from a QM calculation should be
> employed.  This is to be expected, but WHICH method should one use:
> hf/6-31g*, MNDO, something else?
> The standard advice is here
> http://www.gromacs.org/Documentation/How-tos/Parameterization. For
> starters, choose a force field you want to parameterize HCN to work *with*.
> > I know I will have to augment my parameter file to include the new atom
> types and parameters.  But as HCN has a polar hydrogen "on a carbon" how do
> I ensure that this is explicitly maintained?  If I lie and call the hydrogen
> on carbon "H", the designation for an atom bonded to Nitrogen, is this
> enough to keep that hydrogen explicit?  I also want to make a solvent box of
> HCN (cheaper and safer than trying this experimentally!!).  I am assuming
> that simple electrostatics balanced against Van der Waals interactions will
> dictate the proximity of hydrogen bond donor to acceptor in this
> forcefield.
> You seem to be creating problems for yourself by not having a clear
> objective - or at least not expressing it here!
> > Finally, I assume a kluge of non-bonded parameters (van derWaals) is
> reasonable or is there a preferred way of determining an L-J potential?
> Guessing values randomly is likely to get random results. Parameterization
> and validation of parameters are difficult topics to work on, and not
> encouraged for newcomers.
> > If I totally missed the answers to these questions, a hint on better
> keywords or a good reference encompassing these issues would be welcome.
> Mark
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