Thanks a lot Karl, your input parameters will help me much.
Best in peace 🕊️
Cenk
On Fri, Jan 28, 2022, 4:00 PM Karl Kirschner <k.n.kirschner.gmail.com>
wrote:
> Hello Cenk,
>
> In our parameterization work, we perform constraint optimization In
> vacuum (i.e. gas-phase) conditions. In the molecular mechanics constraint
> optimization, we allow everything to relax around the constraint that we
> specified, which matches the gas-phase constraint optimization that was
> done using QM (or DFT). Then, when possible, we validate the resulting
> parameters for usage in solution conditions.
>
> The following is an example from my files that I could find quickly, which
> will start you down a possible path.
>
> *min.in <http://min.in>*:
> Constraint Minimization
> &cntrl
> imin=1, dielc=1,ntb=0,
> maxcyc=20000,
> drms=0.01,nmropt=1,
> cut=40.0,
> &end
> &wt type='END' &end
> LISTOUT=POUT
> DISANG=03.rest
>
> *03.rest*:
> &rst iat = 14, 11, 8, 5,
> r1 = 59.0, r2 = 60.0, r3 = 60.0, r4 = 61.0,
> rk2 = 30000.0, rk3 = 30000.0,
> &end
>
> Of course, there are other approaches like you mention. For example, if you
> computed relative QM energies using implicit solvent, then one might
> consider doing the MM optimization similarly. I hope this helps.
>
> Bests,
> Karl
>
> On Fri, Jan 28, 2022 at 1:30 PM Cenk Andac <cenkandac.gmail.com> wrote:
>
> > Dear Amber community,
> > I have been currently developing amber parameters for a small molecule.
> > Rather than using GAFF, i would like to develop parameters using an AMBER
> > ff.
> > I have already determined resp charges , bond and angle parameters for
> the
> > small molecule. I have also plotted a potential energy curve determined
> at
> > the quantum computations level. I now need to optimize my potential curve
> > by comparing it to non- bonded potentials determined by MM. I used to
> know
> > the procedure back in 2007 and I had saved my sander input parameters for
> > that in my old hard disk. Unfortunately , my hard disk is unreachable and
> > useless now. I don't have the sander input parameters on top of my head.
> > Thus, I kind a got stuck here. My question is I just can't remember if I
> am
> > supposed to do one-step energy computations for increasing steps of the
> > torsions under vacuum or in GB implicit solvent MD conditions.
> > I ll appreciate it much if an amber expert out there could drop the
> > required sander parameters here.
> > Best.
> > Cenk Andac
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Received on Fri Jan 28 2022 - 06:30:02 PST
