[gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

[Ebert Maximilian]

Thanks for the answer. I was checking the CHARMM22 All-Hydrogen Parameter File for Proteins par_all22_prot.inp and the section non-bonded:

nitrogens
N      0.000000  -0.200000     1.850000   0.000000  -0.000100     1.850000 ! ALLOW   PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2    0.000000  -0.200000     1.850000 ! ALLOW   POL
                ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH1    0.000000  -0.200000     1.850000   0.000000  -0.200000     1.550000 ! ALLOW   PEP POL ARO
                ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH2    0.000000  -0.200000     1.850000 ! ALLOW   POL
                ! adm jr.
NH3    0.000000  -0.200000     1.850000 ! ALLOW   POL
                ! adm jr.
NP     0.000000  -0.200000     1.850000 ! ALLOW  PRO
                ! N-terminal proline; from 6-31g* +ProNH2  RLD 9/28/90
NPH    0.000000  -0.200000     1.850000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1    0.000000  -0.200000     1.850000 ! ALLOW ARO
                ! His, adm jr., 9/4/89
NR2    0.000000  -0.200000     1.850000 ! ALLOW ARO
                ! His, adm jr., 9/4/89
NR3    0.000000  -0.200000     1.850000 ! ALLOW ARO
                ! His, adm jr., 9/4/89
NY     0.000000  -0.200000     1.850000 ! ALLOW   ARO
                ! trp, JWK

All nitrogen have the same LJ parameter. I haven’t checked CGenFF but I will definitely look into that. Thanks for you comment.

Max

> On Oct 22, 2015, at 12:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 10/22/15 11:04 AM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I already asked the question in the AMBER list but couldn’t get an answer. So I try my luck here even though it is a bit off topic in the GROMACS list. I was wondering why the different atom types of H, C and O have different LJ-parameter but for all the different types of N we see the identical parameters in OPLS, AMBER and CHARMM?
>> 
> 
> Sometimes that's just the way force fields work out.  Electrostatics are tuned first, and then condensed phase interactions are targeted for LJ refinement. Given the nature of most N interactions (either lone pair or via polar/hydrogen bonding interactions with an H), the electrostatics generally dominate, so a generic LJ parameter that is common to different moieties is sufficient.
> 
> In CGenFF, there are several N types with different LJ, though the biomolecular parts of the CHARMM force field share the same parameters.
> 
> -Justin
> 
> -- 
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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