here is an example from one of my inputs:
source leaprc.protein.ff14SBonlysc
source leaprc.water.opc
loadamberparams frcmod.opc3
x=loadpdb system.gas.pdb
solvateoct x OPC3BOX 10
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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 29 2020 - 09:00:03 PDT
