Hi Giulia,
The 12-6-4 polarization parameters are stored in
$AMBERHOME/dat/leap/parm/lj_1264_pol.dat, and there is no CG atom type
parameter in that file (leading to the error you see).
The solution is to copy that file to your current working directory and add
a line with CG parameters (you can model the parameters based on the other
types that are there -- likely 1.352). Once you add that line, add
`polfile 1264_polfile_copy.dat` to your add12_6_4 ParmEd command.
Hope this helps,
Jason
On Fri, Mar 17, 2023 at 7:56 AM Paiardi, Giulia via AMBER <amber.ambermd.org>
wrote:
> To whom it may concern,
>
>
> I'm parametrizing a protein containing Zn2+ ions and pTYR (pTyr is
> parametrized in ff19SB as PTR) using amber22 with ff19SB and OPC water
> model.?
>
>
> When I add the 12-6-4 Lennard-Jonnes potential for Zn2+ to the protein
> with canonical tyrosine parmed works OK.
>
>
> If I substitute the canonical TYR with PTR (phosphorylated tyr), I can
> still obtain the parameters and the restart file,
>
> however, when adding the 12-6-4 Lennard-Jonnes potential for Zn2+ to the
> parameter file of the complex, parmed gives to me the following error:
>
>
> #################
>
>
> Loaded Amber topology file com.wat.leap.prm7
>
> ['parmedOPC.1264.in']
>
> Reading actions from parmedOPC.1264.in
>
>
> Loading restart file com.wat.leap.rst7
>
> Files are overwritable
>
> Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
> read from
> [/hits/fast/mcm/app/amber/cascade/amber22/dat/leap/parm/lj_1264_pol.dat].
> Using default C4 parameters for water model [OPC].
>
> ***********************************************************
>
> The selected metal ion is Zn
>
> Action add12_6_4 failed
>
> LJ12_6_4Error: Could not find parameters for ATOM_TYPE CG
>
>
> ##################
>
>
> What should I do? Any advise is a great help to me.
>
> ?
>
> Thanks for the help,
>
> Giulia
>
>
>
>
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>
--
Jason M. Swails
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Received on Mon Mar 20 2023 - 13:30:02 PDT
