Many thanks for the suggestion Jason.
Best,
Mish
On Mon, Feb 18, 2019 at 8:37 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Feb 2, 2019 at 9:41 AM mish <smncbr.gmail.com> wrote:
>
> > I tried another workaround for this. Instead of adding hydrogen, I used
> > *parmed* to convert atom CA into hydrogen (HB1) using the following set
> of
> > commands in *parmed:*
> >
> >
> *---------------------------------------------------------------------------------------------------------*
> >
> > parmed -p ../trp.parm7 -c ../trp.rst7 <<EOF
> >
> > #strip backbone atoms
> >
> > strip :1.N,H,HA,C,O
> >
> > #change CA into HB1
> >
> > change atom_name :1.CA HB1
> >
> > change amber_atom_type :1.HB1 HC
> >
> > change mass :1.HB1 1.0080
> >
> > change charge :1.HB1 0.0339
> >
> > change screen :1.HB1 0.8500
> >
> > change ATOMIC_NUMBER :1.HB1 1
> >
> > change radii :1.HB1 1.3000
> >
> > addLJType :1.HB1 radius 1.4870 epsilon 0.0157
> >
> >
> > #cahnge bond angle and dihedrals
> >
> > setbond :1.HB1 :1.CB 340 1.09
> >
> > setAngle :1.HB1 :1.CB :1.HB2 35.0 109.50
> >
> > setAngle :1.HB1 :1.CB :1.HB3 35.0 109.50
> >
> > setAngle :1.HB1 :1.CB :1.CG 50.0 109.50
> >
> >
> > deleteDihedral :1.HB1 :1.CB .CG .CD1
> >
> > deleteDihedral :1.HB1 :1.CB .CG .CD2
> >
> >
> > addDihedral :1.HB1 :1.CB :1.CG :1.CD1 0.00 2.0 0.000 1.2 2.0
> >
> > addDihedral :1.HB1 :1.CB :1.CG :1.CD2 0.00 2.0 0.000 1.2 2.0
> >
> >
> > #change the charge of CB to have overall charge of the unit 0
> >
> > change charge :1.CB -0.0685
> >
> >
> > outparm trp_sidechain.parm7 trp_sidechain.rst7
> >
> > EOF
> >
> > ----------------------------------------------------------------------
> >
> >
> > Everything seems to work fine in the dynamics, but I am still worried if
> > there may not be some hidden mistake, for example, pemed.cuda not reading
> > values from Parm7 file or something like that.
> >
>
> I would suggest calculating the energy using several different programs and
> checking that they're all the same. For instance, if ParmEd (using
> OpenMM), sander, pmemd, pmemd.cuda, and cpptraj (or some combination of
> those options) all give the same results, you can be pretty confident that
> they're all reading the same values.
>
>
> > Moreover, how can we change the value of "Dihedral" using addDihedral of
> > any other command in *parmed*:
> >
>
> There is no command to edit dihedral parameters because dihedrals are
> formally defined by a series of terms (unlike angle and bond terms where
> there is a single term for a single bond/angle). So it's unclear which
> term 'change' would affect.
>
> To change a dihedral, you need to delete the old one and add a new one.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Tue Feb 19 2019 - 10:30:04 PST
