Re: [AMBER] Adding an atom to a residue by parmed

From: mish <>
Date: Sat, 2 Feb 2019 14:40:19 +0000

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



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.

Moreover, how can we change the value of "Dihedral" using addDihedral of
any other command in *parmed*:

 printDihedrals :1.HB1

               Atom 1 Atom 2 Atom 3
  Atom 4 Height Periodic. Phase EEL Scale VDW Scale Dihedral

        1 HB1 ( HC) 2 CB ( CT) 5 CG ( C*) 6 CD1
( CW) 0.0000 2.0000 0.0000 1.2000 2.0000 179.9999


On Fri, Feb 1, 2019 at 3:46 PM mish <> wrote:

> Dear all,
> I am trying to modify amber parm7 files to generate parm7 files for
> amino-acid side-chains in parmed. For this, I first created parm7 and top7
> files of a complete amino-acid in leap (lets say, Trp). Then I deleted
> backbone atoms (.N,H,CA,HA,C,O) and adjusted charge on CB using parmed:
> ------------------------------------------------------------------------
> parmed -p trp.parm7 -c trp.rst7
> strip :1.N,H,CA,HA,C,O
> change charge :1.CB -0.0346
> outparm trp_sidechain.parm7 trp_sidechain.rst7
> -------------------------------------------------------------------------
> Everything seems to work well so far, but I still want to complete valency
> of the CB carbon. Is there any straightforward way in parmed to add way to
> add one more hydrogen (lest say HB1) to atom CB of residue :1 and copy all
> the parameters from HB2 and HB3 in to HB1?
> Best,
> Mish
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Received on Sat Feb 02 2019 - 07:00:02 PST
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