VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 12 2018 - 10:23:41 CST

Hi Joao:
As far as I know, this system was never simulated before. The point is, I
must confess, that it is not clear to me how to best deal with
CGenFF-CHARMM36 in combination, as it occurs on patching. All routes that I
investigated found serious problems.
francesco

On Mon, Nov 12, 2018 at 4:35 PM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi Francesco,
>
> Sorry for the delay in responding to your email. If the molecule that
> you are simulating was simulated before, I would suggest find the
> publication and see how the authors prepared the system and if new
> parameters were published. You might need to parameterize your
> molecule (entirely or partially), and if someone already proposes
> something similar, you can (and should) evaluate if the molecule is
> close enough to yours.
>
> I hope this helps
>
> Best
>
> João
>
>
> On Tue, Oct 23, 2018 at 8:51 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> >
> > Hi Joao:
> > As you suspected, I forgot to change the topology (C8 CG2D1), although
> the parameter .str file was correct (C8 CG321).
> >
> > Amended, however a problem arose on minimization
> > UNABLE TO FIND BOND PARAMETERS FOR CG314 NR3 (ATOMS 6715 3431)
> > 6715 is C9 of the ligand
> > 3431 is NE2 of HSP
> >
> > While nothing was found with CGenFF, with charmm27 someone has proposed
> for methylated histidine (
> https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showthreaded&Number=35082
> )
> >>
> >> BOND
> >> NR3-CT3 261.0 1.49
> >> CT3-HA3 322 1.110
> >> ANGLE
> >> NR3-CT3-HA3 51.5 107.5
> >
> > DIHE
> > NR3-CPH2-NR3-CT3 0 2 180
> > HR2-CPH2-NR3-CT3 0 2 180
> > CPH2-NR3-CT3-HA3 0 0 0
> > HR1-CPH1-NR3-CT3 0 2 180
> > CPH1-NR3-CT3-HA3 0 0 0
> > CPH1-CPH1-NR3-CT3 0 0 0
> >
> >
> > Any better idea? Or calculation of the force constant can not be avoided?
> >
> > thanks
> > francesco
> >
> >
> > On Mon, Oct 22, 2018 at 7:53 PM João Ribeiro <jribeiro_at_ks.uiuc.edu>
> wrote:
> >>
> >> Hi Francesco,
> >>
> >> Unless you changed your topology file, the C8 was defined (in your
> first email) as "ATOM C8 CG2D1 0.098". I don't know how your corrected
> patch looks like but you can change the atom type in the patch, like "ATOM
> 1C8 CG321 -0.124 "
> >>
> >> Whenever you have to change the atom type of a structure, please do it
> at the psfgen level, not changing the psf file.
> >>
> >> Best
> >>
> >> João
> >>
> >>
> >> On Mon, Oct 22, 2018 at 12:08 PM Francesco Pietra <
> chiendarret_at_gmail.com> wrote:
> >>>
> >>> Sorry, (I tried correcting the .psf file by replacing CG2D1 with
> CG32), should be read (I tried correcting the .psf file by replacing CG2D1
> with CG321).
> >>> f
> >>>
> >>> ---------- Forwarded message ---------
> >>> From: Francesco Pietra <chiendarret_at_gmail.com>
> >>> Date: Mon, Oct 22, 2018 at 7:03 PM
> >>> Subject: Re: vmd-l: psfgen patching protein-ligand
> >>> To: <jribeiro_at_ks.uiuc.edu>
> >>> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
> >>>
> >>>
> >>> Hi
> >>> Previously I answered OK, while now problems emerge with minimization--000000000000b663c6057a7a20b5--