[gmx-users] Conversion of charmm36 parameters from namd to gromacs
jalemkul at vt.edu
Sun Dec 3 23:24:07 CET 2017
On 12/3/17 4:18 PM, Daniel Bauer wrote:
> I compared the LJ parameters for the interaction Potassium - backbone
> carbonyl oxygen for CHARMM36 between the Gromacs and NAMD version of the
> forcefield. I found different numbers for the sigma value i cannot
> explain to myself:
> The stock charmm36 implementation has the following LJ parameters for
> potassium and oxygen:
> ; atom Emin (kcal/mol) Rmin/2 (A)
> POT 0.087 1.76375
> O 0.120 1.7
> Converting the above values to units used in gromacs (kJ/mol and nm) and
> applying standard combination rules this should give the following
> nonbonded energy parameters:
> [ pairtypes]
> ; sig = (Rmin,i/2 + Rmin,j/2)/10
> ; eps = sqrt(Emin,i * Emin,j) * 5.184 kcal/kJ
> ; i j func sig (nm) eps (kj/mol)
> O POT 1 0.346 0.4275
> However, the actual entry for the interaction in GROMACS/charmm36 has
> the energy minimum at a much smaller distance (epsilon is on the point
> ; i j func sig (nm) eps (kJ/mol)
> O POT 1 0.282 0.4275
> Can somebody tell me the reason for this huge difference? Is there an
> error in my calculation? I am trying to convert an NBFIX applied to this
> specific interaction to gromacs. However, I am not sure how to proceed
> without doing the reparametrization in gromacs again, because the stock
> values differ that much.
This is actually a value that isn't used. [pairtypes] are for 1-4
interactions, which can never occur between a K+ ion and a carbonyl O.
The inclusion in the list is just because it's really hard to tell our
conversion program to exclude some massive list of impossible
interactions. So they get generated.
But to your point, you're missing a critical point of the CHARMM
parameter format. The full NONBonded parameter entry in
par_all36m_prot.prm for carbonyl O is:
O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000
The last fields are epsilon and Rmin/2 when that atom type is used in a
1-4 interaction. So -0.12/1.7 is for the normal nonbonded interaction,
-0.12/1.4 is for any 1-4 involving O.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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