Hi Elvis
> Alternatively, you can prepare receptor.prmtop and ligand.prmtop using
ante-MMPBSA.py from the complex.prmtop.
What is the command I use to generate the files?
Att.,
Em qua., 6 de mai. de 2020 às 09:26, Elvis Martis <elvis_bcp.elvismartis.in>
escreveu:
> Hi
> All the prmtop files are generated at the beginning.
> Alternatively, you can prepare receptor.prmtop and ligand.prmtop using
> ante-MMPBSA.py from the complex.prmtop.
> The prmtop files do not contain coordinates, so they do not change after
> you have completed all the phases of your simulation.
>
> Your input and commands look good.
> I hope this helps.
> Best Regards
> ElMa
>
>
>
> On Wed, 6 May 2020 at 16:49, Renato Araujo <renatoacufpa.gmail.com> wrote:
>
> > Dear Amber users
> >
> > Please I need help
> >
> > I'm looking to perform the MMGBSA-DECOM calculation as my script mustard.
> >
> > MMGBSA-DECOM
> > &general
> > startframe=47500, endframe=50000, interval=1,
> > verbose=2, keep_files=2, debug_printlevel=2,
> > /
> > &gb
> > igb=5, saltcon=0.0,
> > /
> > &decomp
> > idecomp=2, dec_verbose=1, csv_format=0, print_res="1-306"
> > /
> >
> > According to the command
> > mpirun -np 8 MMPBSA.py -O -i mmpbsa.in -o MMGBSA.dat -do
> DECOMP_MMGBSA.dat
> > -sp complex_solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > ligand.prmtop -y * .mdcrd
> >
> > I need the prmtop files:
> > complex_solvated.prmtop
> > complex.prmtop
> > receiver.prmtop
> > ligand.prmtop
> >
> > My doubt.
> > These prmtop files are generated after the DM production phase or these
> > prmtop files are generated there at the beginning (phases that we are
> > preparing the system to minimize, heat and balance)
> >
> > Any help is welcome
> >
> > Renato Costa
> > Federal Institute of Pará
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed May 06 2020 - 06:30:07 PDT
