[gmx-users] Conversion of charmm36 parameters from namd to gromacs

Daniel Bauer bauer at cbs.tu-darmstadt.de
Mon Dec 4 13:56:08 CET 2017

Hello Justin,

Thanks for your response. I was under the assumption that entries in [
pairtypes ] are the ones that override standard LJ interactions derived
by pairgen. I now know this is a different section.

From what you are saying I come to the conclusion that the POT O
interaction in charmm36 for gromacs have no custom potential but are
derived via combination rules (as they are in namd). Nevertheless, the
numbers still dont seem to match:

Since we can ignore 1-4 Interactions in charmm36 as well as gromacs for
POT-O, the resulting parameters from the namd version are:

sig = 0.3463750 nm; eps=0.42750571533 kJ/mol

However, combining the entries for O and POT in the atomtypes section of
the gromacs version i get something different:

[ atomtypes ]
O          8    15.999000    0.000  A  0.302905564168  0.50208
POT    19    39.098300    0.000  A  0.314264522824  0.36401

sig = 0.308585043 nm; eps=0.42750689 kJ/mol

Again, the epsilon value is matching the namd version while sigma is
still off by about 0.4 A.

If my conversion of the namd parameters and combination rules are
correct, this would be a problem. The different position of the energy
minimum results in a potential energy difference of around 7 kJ/mol for
a distance of 0.29 nm (typical distance for POT-O in the selectivity
filter of potassium channels, see attached image).
Can you give me a source where I can read up on why the values for sigma
and epsilon in gromacs are the way they are? It must be more than a
direct conversion of the numbers from kcal to kJ. Or did I again made a
mistake or took the wrong numbers?

Best regards,

On 12/03/2017 11:23 PM, Justin Lemkul wrote:
> On 12/3/17 4:18 PM, Daniel Bauer wrote:
>> Hello,
>> 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
>> though!)
>> ; 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

Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
bauer at cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.

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