Mark Zottola wrote:
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?
You can specify whatever you want in the topology, as long as you can justify
that it is consistent with the underlying force field model. For instance,
aromatic C-H pairs are represented by explicit hydrogens in the Gromos force fields.
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.
This is a tough task. Much of the Gromos derivation relies on empirical fitting
and tweaking to reproduce condensed-phase behavior. You could start with a few
existing atom types, simulating a box of HCN, and revising based on the results
you get (densities, heat of vaporization, etc). The primary literature on the
derivation of these parameter sets is a bit sparse, but you should be able to
get started.
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.
As is the case for any small molecule :)
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.
I would estimate that 95% of the parameterization questions asked on the list
are posted by people in way over their heads, so it is good to know your
experience level. I would say that the best approach is (unfortunately)
somewhat empirical, but such is the nature of the beast with Gromos force
fields. Some simple QM might give you a start for calculating charges, but as I
understand it, QM was used in the Gromos derivations only to get relative
electron densities around all of the atoms, after which charges were assigned
(empirically) and revised to fit condensed-phase behavior.
-Justin
Thanks again for any help.
On Thu, Jun 3, 2010 at 7:30 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
----- Original Message -----
From: Mark Zottola <[email protected] <mailto:[email protected]>>
Date: Friday, June 4, 2010 1:55
Subject: [gmx-users] Creation of a Non-Standard Residue
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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