On Thu, Sep 6, 2018 at 8:20 AM Sushi Shilpa <sushishilpa.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to create topology and coordinate files for the protein which
> contains Arsenic. I am following 126-LJ non bonded tutorial. I am using
> AMBER 16 and AmberTools 17.
> Here is the tleap.in file
> source leaprc.protein.ff14SB
> source leaprc.gaff
source leaprc.water.spce
> loadamberparams frcmod.ions1lm_126_tip3p
> loadamberparams fcrmod.ionsjc_tip3p
>
Why are you using the SPCE water model, but ions parametrized for the TIP3P
model? You should be using the ion parameters corresponding to the water
model you actually plan to use.
Also, these two frcmod files are *different* ion parameters created by
different groups with different philosophies on which properties to fit
to. You should pick one or the other, but not both. What happens in this
case is that the parameters from the second overwrites the parameters from
the first.
loadoff atomic_ions.lib
> AS = loadmol2 AS.mol2
> mol = loadpdb ArsD120_AS_initial_sele.pdb
> solvatebox mol SPCBOX 8
> addions mol Na+ 0
> savepdb mol As_ArsD.pdb
> saveamberparm mol As_ArsD.prmtop As_ArsD.inpcrd
> quit
>
>
> I have loaded the mol2 file but still I am getting an error mentioned
> below.
> For atom: .R<AS 121>.A<AS 1> Could not find vdW (or other) parameters for
> type: AS
>
The mol2 file is not enough. That's the residue template that provides a
mapping of atoms within residues to specific atom types. You still need to
load parameter files (e.g. parm.dat or frcmod files) that contain
parameters for the atom types defined within the residue templates (like
the mol2).
You can use antechamber to generate a mol2 file for the atoms within
AS.mol2.
HTH,
Jason
--
Jason M. Swails
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Received on Thu Sep 06 2018 - 06:00:03 PDT
