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

Mark Abraham mark.abraham at anu.edu.au
Fri Jun 4 01:30:56 CEST 2010

----- 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.

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