VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 12 2018 - 12:19:08 CST

Francesco,

I'm not sure that what you are attempting is well-advised. I don't think
CGenFF was ever intended for covalent linkage to the protein force field
and I don't think there is any automated path to do so. There is *some*
correspondence between CHARMM36 and CGenFF types and you could notionally
convert CGenFF interactions by matching, but my understanding is that this
has never been suggested by the MacKerell group or others.

You will probably have to find a detailed procedure from the literature to
follow. Unfortunately I have no experience with covalently linked ligands,
so I have no tips to offer there.

HTH,
BKR

On Mon, Nov 12, 2018 at 12:51 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> If residue 1 in the patch is supposed to be HSP, why are you setting the
> type/charge of a likely non-existent atom?
> "ATOM 2NE2 NG2R52 -0.133"
>
> This should probably be ATOM 1NE2, shouldn't it?
>
> -Josh
>
>
> On 2018-11-12 02:02:08-07:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hi:
> I am trying to get bonding between protein HSP NE2 and an organic ligand
> carbon, while imposing CGenFF atom types on both sides.
>
>> PRES ZAHI 1.449 ! patch for ligand to HSP bonding
>> ! Patch must be 1-HSP and 2-ZPN
>> ! use in patch statement
>> ! follow with AUTOgenerate ANGles DIHEdrals command
>> GROUP !
>> ATOM 2C11 CG311 0.332 !
>> ATOM 2C10 CG314 0.199 !
>> ATOM 2H15 HGA1 0.09 !
>> ATOM 2C9 CG2D2 0.127 !
>> ATOM 2C8 CG2O5 0.333 ! CD2--NE2--CE1
>> GROUP ! /
>> ATOM 2CD2 CG2R51 0.219 ! C11--C10--C9--C8
>> ATOM 2NE2 NG2R52 -0.133! |
>> ATOM 2CE1 CG2DC1 0.349 ! H15
>> DELETE ATOM 2H16
>> DELETE ATOM 1HE2
>> BOND 2C10 1NE2
>> IMPR NE2 CD2 CE1 C10
>> IMPR NE2 CE1 CD2 C10
>>
> However, the new atom names are only accepted for the ligand, not for the
> protein, which conserved the original atom types CPH1 NR3 CPH2 for CD2 NE2
> CE1, with bonding between C10 (CG314) and NE2 (NR3). pdb file shows zero
> coordinated for CD2 NE2 CE1 on the ligand residue.
> All that because I am trying to avoid parameterization for unusual bonds,
> such as between CG314 and NR3, although I understand that with atom type
> NG2R52 for NE2 a cascade of problems would arise on the protein side.
> So, which is the best way to associate CGenFF to charmm36?
> thanks
> francesco pietra
>
>