this is odd because a similar command works for me.
Also the list of water models that it gives isn't what I see in the code
for parmed.
Maybe type "which parmed" to check which version you are calling.
Try using the mask for your ions:
> help add12_6_4
add12_6_4 [<ion mask>] [c4file <C4 Param. File> | watermodel <water model>]
[polfile <Pol. Param File> [tunfactor <tunfactor>] [parm
<idx>|<name>]
> add12_6_4 .ZN watermodel OPC
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from [/mnt/raidc2/200/amber22/dat/leap/parm/lj_1264_pol.dat]. Using
default C4 parameters for water model [OPC].
if this doesn't work, send your entire parmed input.
On Tue, Feb 27, 2024 at 11:19 AM Giulio RASTELLI via AMBER <
amber.ambermd.org> wrote:
> Dear Carlos,
>
> the enzyme contains Zn++ and K+ ions.
> To generate and edit the topology file I did the following;
> 1) Sourcing in xleap leaprc.protein.ff19SB, leaprc.opc, and leaprc.gaff2.
> I also loaded frcmod.opc, although I don't think it's required.
> I solvated the system with a periodic box of OPC waters and
> saved the topology.
> 2) In parmed, I gave the command: add12_6_4 watermodel OPC, and I got this
> error message:
> Action add12_6_4 failed
> LJ12_6_4Error: Unrecognized water model OPC; pick one of the following:
> TIP3P, TIP4PEW, SPCE
>
> I understand that the 12_6_4 model for ions can be used with OPC waters, so
> this message is unclear to me.
> I am using the latest version of Amber22 and Ambertools23
>
> Thanks,
> giulio
>
> Il giorno ven 23 feb 2024 alle ore 20:03 Carlos Simmerling <
> carlos.simmerling.gmail.com> ha scritto:
>
> > Hi Giulio,
> > look at this page on the Amber site to see what is currently available
> and
> > what files to load:
> > https://ambermd.org/AmberModels_ions.php
> >
> > Also make sure you are using the most recent AmberTools.
> >
> > On Thu, Feb 22, 2024 at 9:56 AM Giulio RASTELLI via AMBER <
> > amber.ambermd.org> wrote:
> >
> >> Dear all,
> >>
> >> I would like to add 12_6_4 LJ parameters to the topology file describing
> >> an
> >> enzyme containing Zn++ and K+ ions.
> >> The topology was prepared with the ff19SB force field and the OPC water
> >> model.
> >> In parmed I get the following error:
> >> LJ12_6_4Error: Unrecognized water model OPC; pick one of the following:
> >> TIP3P, TIP4PEW, SPCE
> >>
> >> Is it possible to add the 4r term when using the OPC water model?
> >>
> >> Thanks,
> >> giulio
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> _______________________________________________
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Received on Tue Feb 27 2024 - 09:00:02 PST
