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 - 08:30:02 PST
