Re: parameter request for PRES bonding

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Oct 29 2018 - 02:07:38 CDT

I was surprised that parameters were also requested for bonds rather
removed from NE2-C9, such as between C10 and its adjacent C11. Besides
that, requests seemed to be endless, for situations with non-obvious
analogies. So that, with a natural-product ligand, covalently bonded to a
protein receptor, running a decent MD may take months of efforts with QM
calculations.
When that arises as a small part of a large project, involving many
ligand-protein cases, one (myself) becomes frustrated. Unless one decides
that each case is a publication, which, unfortunately, is a decision by
many.
Thanks for your view
francesco

On Mon, Oct 29, 2018 at 12:09 AM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> That seems perfectly normal to me. You changed the atomtypes on C9 and NE2
> (and some others it looks like, but I haven't been following your exploits
> all that closely), so any term that touches those atoms (and there are
> likely a ton of them) will be missing parameters. What behavior did you
> expect?
>
> -Josh
>
>
>
> On 2018-10-27 01:34:07-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> The following PRES generated correctly C9-NE2 bonding between organic
> ligand and HSP of protein
>
>> PRES ZAHI 1.116 ! patch for ligand-HSP bonding
>> ! Patch must be 1-HSP and 2-ZPN
>> ! use in patch statement
>> ! follow with AUTOgenerate ANGles DIHEdrals command
>> GROUP !
>> ATOM 2C10 CG311 0.332 !
>> ATOM 2C9 CG314 0.199 !
>> ATOM 2H91 HGA1 0.09 !
>> ATOM 2C8 CG321 0.127 ! CD2--NE2--CE1
>>
> GROUP ! /
>> ATOM 2CD2 CPH1 0.219 ! C10--C9--C8
>> ATOM 2NE2 NR3 -0.20 ! |
>> ATOM 2CE1 CPH2 0.349 ! H91
>> DELETE ATOM 2H92
>> DELETE ATOM 1HE2
>> BOND 2C9 1NE2
>> IMPR NE2 CD2 CE1 C9
>> IMPR NE2 CE1 CD2 C9
>
> Problems arise, however, on minimization. Besides the expected request for
> BONDS
> CG314 NR3 261.00 1.4900 !
> CG311 HGA2 309.00 1.1110 !
> ANGLES
> HGA1 CG314 NR3 51.5 107.5 !
> CG311 CG314 NR3 117.00 124.00 !
> minimization also required angle
> CG2O5 CG321 CG314
> and many other angles outside the strict area of bonding. Even on
> satisfying these requests, dihedrals were also requested.
> Question: is that normal despite the <AUTOgenerate ANGles DIHEdrals> or
> did I miss something?
> thanks for advice
> francesco pietra
>
>

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