just some typos...
when I refer to "pamr94.dat" I mean "parm99.dat"
when I say "that difference won't affect the simulation", that's because parameters are set to zero or none, which is the same thing...
Best,
Matias
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 29 de Junio 2020 14:03:05
Asunto: Re: [AMBER] ff14SBonlysc + OPC3
Just a follow up to Daniel's and Carlos'...
As OPC3 and TIP3P share the same topology, loading TIP3P and then OPC3 overwrites the former parameters.
Note that "solvent.lib", which is loaded by "leaprc.water.tip3p", contains OP3BOX.
Interesting... if you create a pure water system with and without first loading the protein force filed and then compare the .prmtop files using diff, you may find some differences... that is because TIP3P parameters are also set in "parm99.dat", but they shouldn't. Particularly, I think the following line, which sets HBOND parameters, may be related to that issue:
HW OW 0000. 0000. 4. flag for fast water
In any case, that difference won't affect the simulation as
An additional curiosity, neither "frcmod.opc3" nor "frcmod.tip3p" have angle definitions, I mean there is no angle at all, not even set to zero! however leap doesn't complain about that... My guess is that leap hard-codes some instructions to avid giving an error message and setting angle parameters to fast water models... That's important, because "pamr94.dat" does define angles for TIP3P, but they aren't printed to the topology.
Last, but not least... in case you are using divalent ions, you may consider reading this just accepted JCTC:
Systematic Parameterization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
[
https://doi.org/10.1021/acs.jctc.0c00194]
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Daniel Roe" <daniel.r.roe.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 29 de Junio 2020 12:25:38
Asunto: Re: [AMBER] ff14SBonlysc + OPC3
Hi,
Not really - the parameters for OPC3 are in frcmod.opc3 - just loading
the OPC3BOX won't do it. I just checked and it seems that there is no
leaprc.water.OPC3 in $AMBERHOME/dat/leaprc/cmd, which seems like an
oversight. However, if you check leaprc.water.OPC and
leaprc.water.tip3p, they give you clues to how you would load opc3
parameters.
Here's what I would do, but full disclaimer: I've never tested this,
so others who are smarter may have better recommendations. I would use
leaprc.water.OPC as a template (copy to a new file), replace
frcmod.opc with frcmod.opc3, and use the ions from the tip3p file,
e.g.:
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = OPC
WAT = OPC
loadAmberParams frcmod.opc3
loadAmberParams frcmod.ions1lm_126_tip3p
loadAmberParams frcmod.ionsjc_tip3p
loadAmberParams frcmod.ions234lm_126_tip3p
Hope this helps,
-Dan
On Mon, Jun 29, 2020 at 8:40 AM Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
> Dear community,
>
> I am a little confused on the usage of OPC3 water model. I am trying to update my tleap files to use ff14SBonlysc + OPC3BOX water forcefields for my runs, but I am not sure how to source everything correctly. This is the leap input I wrote, which works, but if I don’t include source leaprc.water.tip3p, it doesn’t. As shown below I am loading the tip3p model, with a OPC3 box, is that correct?
>
> I tried with a leaprc.water.opc3 command but it gives an error. Also If I add the loadAmberParams frcmod.opc3 to the input file, again it works, but I am not sure I am doing the right thing.
>
> Can anybody please enlighten me?
> I read the manual, but it is really a little tricky.
>
> Thanks!!
> Fabian
>
> ==== tleap input ===
>
> source leaprc.protein.ff14SBonlysc
> source leaprc.water.tip3p
>
> loadAmberParams frcmod.ionsjc_tip3p
> set default PBradii mbondi3
>
> MOL1 = loadpdb 6HD5.TU.scwrl4.molprobity.clean.pdb
>
> savepdb MOL1 com.nata.YEAST.6HD5.20A.opc3.dry.pdb
> saveamberparm MOL1 com.nata.YEAST.6HD5.20A.opc3.dry.prmtop com.nata.YEAST.6HD5.20A.opc3.dry.rst7
>
> solvateoct MOL1 OPC3BOX 20
>
> addions MOL1 Na+ 0
> addions MOL1 Cl- 0
>
> savepdb MOL1 com.nata.YEAST.6HD5.20A.solv.pdb
> saveamberparm MOL1 com.nata.YEAST.6HD5.20A.solv.prmtop com.nata.YEAST.6HD5.20A.solv.rst7
>
> quit
>
>
> Best,
>
> Fabian
>
> Fabian Glaser PhD
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
> Tel +972 (0) 4 8293701
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jun 29 2020 - 10:30:04 PDT
