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 Mon Feb 18 2019 - 13:00:02 PST
