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

Mark Zottola mzottola at gmail.com
Thu Jun 3 17:53:10 CEST 2010

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?

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

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?

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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