On 7/19/18 11:54 PM, Joshua Cummings wrote:
Hi Everyone,
I'm currently trying to run some simulations that involve the absorption of N2
into a liquid solvent. I'm having some difficulty in generating the topology
for N2. For reference, the pdb file I have for N2 is as follows:
HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 N
HETATM2 N6A HDZ 0 0.000 0.000 -0.553 1.00 0.00 N
CONECT12
CONECT21
END
When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs
doesn't recognise the residue. I've tried using both the LigParGen server and
the PRODRG to generate the topology, but neither work. PRODRG generates an
error saying it does not deal with mono/di-atomic molecules and LigParGen won't
recognise N2 at all.
I haven't had any trouble generating topologies for other small gas molecules
such as CH4, am I missing something here or are OPLS parameters not possible
for N2? Should I use some other forcefield for N2?
There should be parameters in the literature for N2, perhaps not for
OPLS-AA (the "L" is for "liquid," after all, and focuses on biomolecules
and analogs) but might give you a place to start. In principle, the
parametrization is pretty straightforward. The charges are zero, the
bond length and vibrational frequency can be easily computed via QM if
not determined experimentally via spectroscopy, and then you need to fit
the LJ parameters to reproduce either liquid density/RDF at low
temperature, free energy of solvation (if known), etc.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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