Hi Giulio,
I tested your prmtop in my version of parmed and it seems to work fine for
me:
Loaded Amber topology file 5edu_ff19_opc.top
Reading input from STDIN...
> 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].
***********************************************************
The selected metal ion is Zn
I still suspect that you aren't using a recent parmed/AmberTools.
maybe add to your parmed script this help command, and you should see OPC
listed as an option:
> 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>]
Adds the LENNARD_JONES_CCOEF term for the ion 12-6-4 Lennard-Jones
potential
term. If provided, the mask will allow you to specify which ions. If not
provided, :ZN will be used for the mask by default. The C4 parameter
between
the ion and water can either be taken from the references for the
requested
[watermodel] (TIP3P, TIP4PEW, SPCE, OPC3, OPC, FB3, and FB4)
Carlos
On Wed, Feb 28, 2024 at 10:14 AM Giulio RASTELLI <giulio.rastelli.unimore.it>
wrote:
> Dear Carlos,
> parmed points to the correct executable.
>
> In parmed, I tried all these commands:
> add12_6_4 watermodel OPC
> add12_6_4 .ZN watermodel OPC
> add12_6_4 :ZN watermodel OPC
> add12_6_4 .%Zn2+ watermodel OPC
>
> But in all cases I get this:
> Action add12_6_4 failed
> LJ12_6_4Error: Unrecognized water model OPC; pick one of the following:
> TIP3P, TIP4PEW, SPCE
>
> Don't know how to get rid of this problem.
> If I load frcmod.ionslm_1264_opc within xleap I obtain a different
> topology file (though I have to check if the diff
> reflects correctly modified parameters).
>
> Thanks,
> giulio
>
>
> Il giorno mar 27 feb 2024 alle ore 17:34 Carlos Simmerling <
> carlos.simmerling.gmail.com> ha scritto:
>
>> 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
>>> >>
>>> >
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 04 2024 - 10:00:03 PST
