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
>
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Received on Mon Jun 29 2020 - 08:30:06 PDT
