[gmx-users] Atom types comparison between CGenFF and Charm36FF

[Mohsen Ramezanpour]

Thanks Justin for your comment.

I have a bit of difficulty for the finding the analog parts to these two
parts.

Is there any database (preferably with shapes) for the molecules available
in charmmFF?

Cheers,
Mohsen

On Tue, Jun 27, 2017 at 7:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/27/17 3:27 PM, Mohsen Ramezanpour wrote:
>
>> Dear Gromacs Users,
>>
>> I am trying to parameterize a molecule in Charmm36FF.
>>
>> As part of this molecule, there is a "neutral trimethylamine nitrogen" and
>> its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively.
>>
>> To have some idea about the appropriate atom types, I first used the
>> GAAMP server.
>>
>> Here are the assigned atom types by GAAMP (based on CGenFF force field):
>>
>>
>> *For Neutral case:*
>> NG301 for N,
>> CG3AM0 for two methyl group connected to the N, i.e for bolded Carbons in
>> C-N-*C(2).*
>> HGA3 for each Hydrogen atom in CG3AM0 methyl groups,
>> CG321 for the carbon atom connecting the NC(2) to the rest of molecule.
>> i.e. for bolded Carbon in *C*-N-C(2),
>> and HGA2 for the Hydrogen atoms connected to CG321.
>> ###############################
>>
>> *For Protonated case:*
>> NG3P1 for N,
>> CG334 for two methyl group connected to the N, i.e for bolded Carbons in
>> C-N(H)-*C(2).*
>> HGA3 for each Hydrogen atom in CG334 methyl groups,
>> CG324 for the carbon atom connecting the NC(2) to the rest of molecule.
>> i.e. for bolded Carbon in *C*-N(H)-C(2),
>> and HGA2 for the Hydrogen atoms connected to CG321.
>> ################################
>>
>> Now, I want to find the best equivalent atom type in Charmm36FF for each
>> case.
>>
>> For the protonated case, I think it is easier as it is something between
>> PE
>> and PC lipid headgroups. For the neutral case, however, it is difficult to
>> find similar atom types in Charmm36.
>>
>> My approach was to check the LJ and bonded parameters for the assigned
>> atom
>> types (which are in CGenFF) and find the atom types in Charmm36 with the
>> exact same values. Although possible for some cases, but there are many
>> problems with this approach:
>>
>> 1) the exact values are not found in Charmm36FF.
>> 2) If it is found, there are a lot of parameters missing in the Charmm36FF
>> force field. Not all the bonds, angles, and dihedrals are defined in
>> Charmm36FF.
>>
>> Thanks in advance for any comment or suggestion.
>>
>>
> The "G" in CGenFF is for "general," which means the parameters are not
> necessarily the same as the parent CHARMM force field, and are subsequently
> a compromise between being highly optimized (e.g. CHARMM36) and being
> broadly applicable (general) such that the types can be used across
> different molecules.
>
> If you want to parametrize something for CHARMM, e.g. to be merged into a
> larger molecule, you're wasting your time with trying to generate a CGenFF
> topology and try to find exact matches in CHARMM36.  By definition, you
> won't.  If your goal is a CHARMM topology, then start from existing CHARMM
> atom types, import charges by analogy, and do a full parametrization
> procedure (well described in numerous places in the literature).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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